Pseudogenes and uses thereof

ABSTRACT

The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to pseudogenes as diagnostic markers and clinical targets for prostate cancer.

This application claims priority U.S. Provisional Application No. 61/577,767, filed on Dec. 20, 2011, which is herein incorporated by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under CA132874 and CA111275 awarded by the National Institutes of Health and W81XWH-08-1-0110 awarded by the Army Medical Research and Materiel Command. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to pseudogenes as diagnostic markers and clinical targets for cancer.

BACKGROUND OF THE INVENTION

Afflicting one out of nine men over age 65, prostate cancer (PCA) is a leading cause of male cancer-related death, second only to lung cancer (Abate-Shen and Shen, Genes Dev 14:2410 [2000]; Ruijter et al., Endocr Rev, 20:22 [1999]). The American Cancer Society estimates that about 184,500 American men will be diagnosed with prostate cancer and 39,200 will die in 2001.

Prostate cancer is typically diagnosed with a digital rectal exam and/or prostate specific antigen (PSA) screening. An elevated serum PSA level can indicate the presence of PCA. PSA is used as a marker for prostate cancer because it is secreted only by prostate cells. A healthy prostate will produce a stable amount—typically below 4 nanograms per milliliter, or a PSA reading of “4” or less—whereas cancer cells produce escalating amounts that correspond with the severity of the cancer. A level between 4 and 10 may raise a doctor's suspicion that a patient has prostate cancer, while amounts above 50 may show that the tumor has spread elsewhere in the body.

When PSA or digital tests indicate a strong likelihood that cancer is present, a transrectal ultrasound (TRUS) is used to map the prostate and show any suspicious areas. Biopsies of various sectors of the prostate are used to determine if prostate cancer is present. Treatment options depend on the stage of the cancer. Men with a 10-year life expectancy or less who have a low Gleason number and whose tumor has not spread beyond the prostate are often treated with watchful waiting (no treatment). Treatment options for more aggressive cancers include surgical treatments such as radical prostatectomy (RP), in which the prostate is completely removed (with or without nerve sparing techniques) and radiation, applied through an external beam that directs the dose to the prostate from outside the body or via low-dose radioactive seeds that are implanted within the prostate to kill cancer cells locally. Anti-androgen hormone therapy is also used, alone or in conjunction with surgery or radiation. Hormone therapy uses luteinizing hormone-releasing hormones (LH-RH) analogs, which block the pituitary from producing hormones that stimulate testosterone production. Patients must have injections of LH-RH analogs for the rest of their lives.

While surgical and hormonal treatments are often effective for localized PCA, advanced disease remains essentially incurable. Androgen ablation is the most common therapy for advanced PCA, leading to massive apoptosis of androgen-dependent malignant cells and temporary tumor regression. In most cases, however, the tumor reemerges with a vengeance and can proliferate independent of androgen signals.

The advent of prostate specific antigen (PSA) screening has led to earlier detection of PCA and significantly reduced PCA-associated fatalities. However, the impact of PSA screening on cancer-specific mortality is still unknown pending the results of prospective randomized screening studies (Etzioni et al., J. Natl. Cancer Inst., 91:1033 [1999]; Maattanen et al., Br. J. Cancer 79:1210 [1999]; Schroder et al., J. Natl. Cancer Inst., 90:1817 [1998]). A major limitation of the serum PSA test is a lack of prostate cancer sensitivity and specificity especially in the intermediate range of PSA detection (4-10 ng/ml). Elevated serum PSA levels are often detected in patients with non-malignant conditions such as benign prostatic hyperplasia (BPH) and prostatitis, and provide little information about the aggressiveness of the cancer detected. Coincident with increased serum PSA testing, there has been a dramatic increase in the number of prostate needle biopsies performed (Jacobsen et al., JAMA 274:1445 [1995]). This has resulted in a surge of equivocal prostate needle biopsies (Epstein and Potter J. Urol., 166:402 [2001]). Thus, development of additional serum and tissue biomarkers to supplement PSA screening is needed.

SUMMARY OF THE INVENTION

The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to pseudogenes as diagnostic markers and clinical targets for cancer.

Embodiments of the present invention provide compositions, kits, and methods useful in the detection and screening of prostate and breast cancer.

For example, embodiments of the present invention provide a method of screening for the presence of breast cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of a pseudogene (e.g., ATPase, aminophospholipid transporter, class I, type 8A, member 2 pseudogene (ATP8A2-Ψ) or dipeptidyl-peptidase 3 (DPP3)); and detecting the level of expression of the pseudogene in the sample using an in vitro assay, wherein an increased level of expression of the pseudogene in the sample relative to the level in normal breast cells is indicative of breast cancer in the subject. In some embodiments, the sample is, for example, blood, plasma, serum or breast cells. In some embodiments, detection is carried out utilizing a method selected from, for example, a sequencing technique, a nucleic acid hybridization technique, a nucleic acid amplification technique (e.g., polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification or nucleic acid sequence based amplification) or an immunoassay. In some embodiments, the reagent is, for example, a pair of amplification oligonucleotides or an oligonucleotide probe. In some embodiments, the breast cancer is luminal breast cancer.

In some embodiments, the present invention provides a method of screening for the presence of prostate cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of a pseudogene (e.g., coxsackie virus and adenovirus receptor pseudogene (CXADR-Ψ), NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9 (NDUFA9), epithelial cell adhesion molecule (EPCAM), PDGFA associated protein 1 (PDAP1), RNA binding motif protein 17 (RBM17), carboxylesterase 5A (CES7) or kallikrein-related peptidase 4-kallikrein pseudogene 1 (KLK4-KLKP1)); and detecting the level or presence of expression of the pseudogene in the sample using an in vitro assay, wherein the presence or an increased level of expression of the pseudogene in the sample relative to the level in normal prostate cells is indicative of prostate cancer in the subject. In some embodiments, the sample is, for example, tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions or prostate cells. In some embodiments, detection is carried out utilizing a method selected from, for example, a sequencing technique, a nucleic acid hybridization technique, a nucleic acid amplification technique (e.g., polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification or nucleic acid sequence based amplification) or an immunoassay. In some embodiments, the reagent is, for example, a pair of amplification oligonucleotides or an oligonucleotide probe. In some embodiments, the cancer is localized prostate cancer or metastatic prostate cancer.

Additional embodiments are described herein.

DESCRIPTION OF THE FIGURES

FIG. 1 shows the pseudogene expression analysis pipeline.

FIG. 2 shows a schematic representation of cluster alignments with pseudogene transcripts shown for ATP8A2-Ψ and CXADR-Ψ.

FIG. 3 shows tissue-specific pseudogene expression profiles. A heatmap of pseudogene expression sorted on the basis of tissue specific expression displays tissue specific (top), tissue-enriched/non-specific (middle) and ubiquitously expressed pseudogenes (bottom).

FIG. 4 shows cancer-specific pseudogene expression profiles. A heatmap of pseudogene expression sorted according to cancer-specific expression patterns displays pseudogene transcripts specific to individual cancers (top), common across multiple cancers (tissueenriched; middle) and non-specific (bottom).

FIG. 5 shows expression of CXADR-Ψ in prostate cancer. (A) A histogram of expression values (y-axis) of CXADR-Ψ (top) and CXADR-parental (bottom) across a panel of prostate and other tissue samples (x-axis). (B) A summary histogram of the expression values of CXADR-Ψ and CXADR-parental in prostate cancers either harboring or lacking an ETS transcription factor gene fusion, or in nonprostate samples (left). On the right, expression of CXADR-Ψ and CXADR-parental in matched pairs of tumor and benign samples from prostate cancer patients (right).

FIG. 6 shows expression of ATP8A2-Ψ in breast cancer. Histograms of Taqman assay based qRT-PCR expression profiles of (A) ATP8A2-Ψ and (B) ATP8A2-wild type, across a panel of samples from breast and other tissue types as indicated. (Inset) A summary histogram of the expression values of ATP8A2-Ψ and ATP8A2-parental in breast cancer samples relative to benign breast and other tissues (left) and luminal vs. basal breast cancer subtypes (right). (C) Cell proliferation assays following siRNA based knockdowns of ATP8A2-wild type and pseudogene as indicated. (D) Histogram of Boyden chamber assay showing cell migration (left) and invasion through matrigel (right). (E) The effect of ATP8A2 pseudogene overexpression in TERT-HMEC cells on cell proliferation (left) and cell migration based on Incucyte wound confluency assay (right) and (F) Chicken chorioallantoic membrane assay of HCC-1806 cells treated with either non-targeting control siRNA, ATP8A2-WT siRNA or ATP8A2-Ψ siRNA showing relative number of cells intravaseted in the lower CAM (left) and metastatic cells in chicken lung (right).

FIG. 7 shows samples comprising the transcriptome sequencing data compendium. (A) Pie chart showing relative distribution of samples from each tissue type (Right); Bar chart representing the numbers of samples in the indicated categories, in each tissue type. (B) Table indicating exact number of samples in each sub-category with a summary of passed purity filter (PF) read count. MPN: Multiple primary neoplasia.

FIG. 8 shows a comparision of pseudogene annotations with reference databases (Yale and ENCODE). A. Venn diagrams showing overlaps between clusters/probes (left), pseudogenes (middle) and genes (right) based on Yale, ENCODE, and BLAT based custom analysis. B. Clusters not overlapped with reference databases were assessed for proximity to existing pseudogenes. (Left) Graphical representation of number of pseudogenes (y-axis) corresponding to unmapped clusters that are in defined proximity (x-axis) to existing pseudogenes. (Right) UCSC tracks display CENTG2 and HNRNPA1 pseudogenes with chromosomal coordinates based on ENCODE Gencode Manual Gene Annotations, immediately flanked by pseudogene clusters identified by Custom BLAT analysis.

FIG. 9 shows a scatter plot reprsentation of the correlation between the total number of pseudogenes observed in a sequencing run (x-axis) with the sequence yield (Passed Filter reads) (y-axis).

FIG. 10 shows an intersection plot displaying the fraction of pseudogene transcripts with corresponding chromosomal loci enriched for H3K4me3 in breast cancer cell line MCF7.

FIG. 11 shows a correlation between gene and pseudogene pairs.

FIG. 12 shows a scatter plot representation of correlation between expression levels of (A) ATP8A2 and (B) CXADR pseudogenes as assessed by RNA-seq (y-axis) and qPCR (x-axis).

FIG. 13 shows a sequence alignment of ATP8A2-WT and -Ψ (top) and CXADR-WT and -Ψ (bottom) using Mulialign interface.

FIG. 14 shows cloning and sequencing of CXADR-Ψ from prostate cancer samples. A. Two prostate cancer tissues used to amplify ˜300 bp bands corresponding to CXADR-Ψ cDNA. B. The sequence of prostate cancer tissue derived CXADR-Ψ cDNA aligned to reference CXADR-Ψ sequence. C. The sequence of prostate cancer tissue derived CXADR-Ψ cDNA aligned to wild type CXADR-Ψ sequence.

FIG. 15 shows (A) Estimation of ATP8A2-WT and -pseudogene transcripts by Taqman qPCR assay. (B) Western blot analysis of ATP8A2 in the three breast cell lines. (C) qPCR analysis of levels of ATP8A2-wt and pseudogene transcripts after siRNA knockdown in Cama-1 and HCC1806 cells. (D) Cell Proliferation Assays following siRNA based knockdowns of ATP8A2-wild type and pseudogene in the pancreatic cancer cell line BXPC3. (E) Western blot analysis of breast cancer cell line HCC1806 knocked down for ATP8A2-wild type or pseudogene siRNA probed with ATP8A2 antibody.

FIG. 16 shows a prostate cancer specific chimeric transcript involving the pseudogene KLKP1. (a) Histogram of expression values of KLK4-KLKP1 chimera across a panel of prostate and other tissue samples as indicated. The inset shows KLK4-KLKP1 chimeric transcript architecture based on transcriptome sequencing. (b) Predicted amino acid sequence of the KLK4-KLKP1 open reading frame indicating the stretch of novel peptide encoded by KLKP1_.

FIG. 17 shows the nucleic acid sequences of CXADR_Ψ (SEQ ID NO:12), ATP8A2_Ψ_ENST00000420453 (SEQ ID NO:13), NDUFA9_Ψ_ENST00000436210 (SEQ ID NO:14), DPP3_Ψ_ENST00000416030 (SEQ ID NO:15), CES7_Ψ (SEQ ID NO:16), PDAP1_Ψ_ENST00000392530 (SEQ ID NO:17), CENTG2_Ψ_ENST00000427215 (SEQ ID NO:18), NF1_Ψ (SEQ ID NO:19), PGK1_Ψ_ENST00000431702 (SEQ ID NO:20), CRIP1_Ψ_ENST00000442565 (SEQ ID NO:21), MTCH1_Ψ (SEQ ID NO:22), PPP4R2_Ψ_ENST00000429866 (SEQ ID NO:23), TMEM161B_Ψ_ENST00000457388 (SEQ ID NO:24), PTPN2_Ψ_ENST00000433704 (SEQ ID NO:25), SCYL2_Ψ_ENST00000392253 (SEQ ID NO:26), KLK4-KLKP1 (Pseudogene Readthrough) (SEQ ID NO:27).

DEFINITIONS

To facilitate an understanding of the present invention, a number of terms and phrases are defined below:

As used herein, the terms “detect”, “detecting” or “detection” may describe either the general act of discovering or discerning or the specific observation of a detectably labeled composition.

As used herein, the term “subject” refers to any organisms that are screened using the diagnostic methods described herein. Such organisms preferably include, but are not limited to, mammals (e.g., murines, simians, equines, bovines, porcines, canines, felines, and the like), and most preferably includes humans.

The term “diagnosed,” as used herein, refers to the recognition of a disease by its signs and symptoms, or genetic analysis, pathological analysis, histological analysis, and the like.

A “subject suspected of having cancer” encompasses an individual who has received an initial diagnosis (e.g., a CT scan showing a mass or increased PSA level) but for whom the stage of cancer or presence or absence of pseudogenes indicative of cancer is not known. The term further includes people who once had cancer (e.g., an individual in remission). In some embodiments, “subjects” are control subjects that are suspected of having cancer or diagnosed with cancer.

As used herein, the term “characterizing cancer in a subject” refers to the identification of one or more properties of a cancer sample in a subject, including but not limited to, the presence of benign, pre-cancerous or cancerous tissue, the stage of the cancer, and the subject's prognosis. Cancers may be characterized by the identification of the expression of one or more cancer marker genes, including but not limited to, the pseudogenes disclosed herein.

As used herein, the term “characterizing prostate tissue in a subject” refers to the identification of one or more properties of a prostate tissue sample (e.g., including but not limited to, the presence of cancerous tissue, the presence or absence of pseudogenes, the presence of pre-cancerous tissue that is likely to become cancerous, and the presence of cancerous tissue that is likely to metastasize). In some embodiments, tissues are characterized by the identification of the expression of one or more cancer marker genes, including but not limited to, the cancer markers disclosed herein.

As used herein, the term “stage of cancer” refers to a qualitative or quantitative assessment of the level of advancement of a cancer. Criteria used to determine the stage of a cancer include, but are not limited to, the size of the tumor and the extent of metastases (e.g., localized or distant).

As used herein, the term “nucleic acid molecule” refers to any nucleic acid containing molecule, including but not limited to, DNA or RNA. The term encompasses sequences that include any of the known base analogs of DNA and RNA including, but not limited to, 4-acetylcytosine, 8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine, 5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarbonylmethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, N-uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and 2,6-diaminopurine.

The term “gene” refers to a nucleic acid (e.g., DNA) sequence that comprises coding sequences necessary for the production of a polypeptide, precursor, or RNA (e.g., rRNA, tRNA). The polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragments are retained. The term also encompasses the coding region of a structural gene and the sequences located adjacent to the coding region on both the 5′ and 3′ ends for a distance of about 1 kb or more on either end such that the gene corresponds to the length of the full-length mRNA. Sequences located 5′ of the coding region and present on the mRNA are referred to as 5′ non-translated sequences. Sequences located 3′ or downstream of the coding region and present on the mRNA are referred to as 3′ non-translated sequences. The term “gene” encompasses both cDNA and genomic forms of a gene. A genomic form or clone of a gene contains the coding region interrupted with non-coding sequences termed “introns” or “intervening regions” or “intervening sequences.” Introns are segments of a gene that are transcribed into nuclear RNA (hnRNA); introns may contain regulatory elements such as enhancers. Introns are removed or “spliced out” from the nuclear or primary transcript; introns therefore are absent in the messenger RNA (mRNA) transcript. The mRNA functions during translation to specify the sequence or order of amino acids in a nascent polypeptide.

As used herein, the term “oligonucleotide,” refers to a short length of single-stranded polynucleotide chain. Oligonucleotides are typically less than 200 residues long (e.g., between 15 and 100), however, as used herein, the term is also intended to encompass longer polynucleotide chains. Oligonucleotides are often referred to by their length. For example a 24 residue oligonucleotide is referred to as a “24-mer”. Oligonucleotides can form secondary and tertiary structures by self-hybridizing or by hybridizing to other polynucleotides. Such structures can include, but are not limited to, duplexes, hairpins, cruciforms, bends, and triplexes.

As used herein, the terms “complementary” or “complementarity” are used in reference to polynucleotides (i.e., a sequence of nucleotides) related by the base-pairing rules. For example, the sequence “5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.” Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, as well as detection methods that depend upon binding between nucleic acids.

The term “homology” refers to a degree of complementarity. There may be partial homology or complete homology (i.e., identity). A partially complementary sequence is a nucleic acid molecule that at least partially inhibits a completely complementary nucleic acid molecule from hybridizing to a target nucleic acid is “substantially homologous.” The inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or Northern blot, solution hybridization and the like) under conditions of low stringency. A substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous nucleic acid molecule to a target under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction. The absence of non-specific binding may be tested by the use of a second target that is substantially non-complementary (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second non-complementary target.

As used herein, the term “hybridization” is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is impacted by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, the T_(m) of the formed hybrid, and the G:C ratio within the nucleic acids. A single molecule that contains pairing of complementary nucleic acids within its structure is said to be “self-hybridized.”

As used herein the term “stringency” is used in reference to the conditions of temperature, ionic strength, and the presence of other compounds such as organic solvents, under which nucleic acid hybridizations are conducted. Under “low stringency conditions” a nucleic acid sequence of interest will hybridize to its exact complement, sequences with single base mismatches, closely related sequences (e.g., sequences with 90% or greater homology), and sequences having only partial homology (e.g., sequences with 50-90% homology). Under “medium stringency conditions,” a nucleic acid sequence of interest will hybridize only to its exact complement, sequences with single base mismatches, and closely relation sequences (e.g., 90% or greater homology). Under “high stringency conditions,” a nucleic acid sequence of interest will hybridize only to its exact complement, and (depending on conditions such a temperature) sequences with single base mismatches. In other words, under conditions of high stringency the temperature can be raised so as to exclude hybridization to sequences with single base mismatches.

The term “isolated” when used in relation to a nucleic acid, as in “an isolated oligonucleotide” or “isolated polynucleotide” refers to a nucleic acid sequence that is identified and separated from at least one component or contaminant with which it is ordinarily associated in its natural source. Isolated nucleic acid is such present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids as nucleic acids such as DNA and RNA found in the state they exist in nature. For example, a given DNA sequence (e.g., a gene) is found on the host cell chromosome in proximity to neighboring genes; RNA sequences, such as a specific mRNA sequence encoding a specific protein, are found in the cell as a mixture with numerous other mRNAs that encode a multitude of proteins. However, isolated nucleic acid encoding a given protein includes, by way of example, such nucleic acid in cells ordinarily expressing the given protein where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature. The isolated nucleic acid, oligonucleotide, or polynucleotide may be present in single-stranded or double-stranded form. When an isolated nucleic acid, oligonucleotide or polynucleotide is to be utilized to express a protein, the oligonucleotide or polynucleotide will contain at a minimum the sense or coding strand (i.e., the oligonucleotide or polynucleotide may be single-stranded), but may contain both the sense and anti-sense strands (i.e., the oligonucleotide or polynucleotide may be double-stranded).

As used herein, the term “purified” or “to purify” refers to the removal of components (e.g., contaminants) from a sample. For example, antibodies are purified by removal of contaminating non-immunoglobulin proteins; they are also purified by the removal of immunoglobulin that does not bind to the target molecule. The removal of non-immunoglobulin proteins and/or the removal of immunoglobulins that do not bind to the target molecule results in an increase in the percent of target-reactive immunoglobulins in the sample. In another example, recombinant polypeptides are expressed in bacterial host cells and the polypeptides are purified by the removal of host cell proteins; the percent of recombinant polypeptides is thereby increased in the sample.

As used herein, the term “sample” is used in its broadest sense. In one sense, it is meant to include a specimen or culture obtained from any source, as well as biological and environmental samples. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues, and gases. Biological samples include blood products, such as plasma, serum and the like. Such examples are not however to be construed as limiting the sample types applicable to the present invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to pseudogenes as diagnostic markers and clinical targets for prostate cancer.

For example, in some embodiments, ATP8A2-Ψ and DPP3 pseudogenes were identified as being specific to breast cancer and CXADR-Ψ, NDUFA9, EPCAM, PDAP1, RBM17 and CES7 pseudogenes and the KLK4-KLKP1 fusion were identified as being specific to prostate cancer. Sequences of exemplary pseudogenes are shown in FIG. 17.

I. Diagnostic and Screening Methods

As described above, embodiments of the present invention provide diagnostic and screening methods that utilize the detection of pseudogenes (e.g., ATP8A2-Ψ, DPP3, CXADR-Ψ, NDUFA9, EPCAM, PDAP1, RBM17, CES7 and KLK4-KLKP1). Exemplary, non-limiting methods are described below.

Any patient sample suspected of containing the pseudogenes may be tested according to methods of embodiments of the present invention. By way of non-limiting examples, the sample may be tissue (e.g., a prostate biopsy sample or a tissue sample obtained by prostatectomy), blood, urine, semen, prostatic secretions or a fraction thereof (e.g., plasma, serum, urine supernatant, urine cell pellet or prostate cells). A urine sample is preferably collected immediately following an attentive digital rectal examination (DRE), which causes prostate cells from the prostate gland to shed into the urinary tract.

In some embodiments, the patient sample is subjected to preliminary processing designed to isolate or enrich the sample for the pseudogenes or cells that contain the pseudogenes. A variety of techniques known to those of ordinary skill in the art may be used for this purpose, including but not limited to: centrifugation; immunocapture; cell lysis; and, nucleic acid target capture (See, e.g., EP Pat. No. 1 409 727, herein incorporated by reference in its entirety).

The pseudogenes may be detected along with other markers in a multiplex or panel format. Markers are selected for their predictive value alone or in combination with the pseudogenes. Exemplary prostate cancer markers include, but are not limited to: AMACR/P504S (U.S. Pat. No. 6,262,245); PCA3 (U.S. Pat. No. 7,008,765); PCGEM1 (U.S. Pat. No. 6,828,429); prostein/P501S, P503S, P504S, P509S, P510S, prostase/P703P, P710P (U.S. Publication No. 20030185830); RAS/KRAS (Bos, Cancer Res. 49:4682-89 (1989); Kranenburg, Biochimica et Biophysica Acta 1756:81-82 (2005)); and, those disclosed in U.S. Pat. Nos. 5,854,206 and 6,034,218, 7,229,774, each of which is herein incorporated by reference in its entirety. Markers for other cancers, diseases, infections, and metabolic conditions are also contemplated for inclusion in a multiplex or panel format.

i. DNA and RNA Detection

The pseudogenes of the present invention are detected using a variety of nucleic acid techniques known to those of ordinary skill in the art, including but not limited to: nucleic acid sequencing; nucleic acid hybridization; and, nucleic acid amplification.

1. Sequencing

Illustrative non-limiting examples of nucleic acid sequencing techniques include, but are not limited to, chain terminator (Sanger) sequencing and dye terminator sequencing. Those of ordinary skill in the art will recognize that because RNA is less stable in the cell and more prone to nuclease attack experimentally RNA is usually reverse transcribed to DNA before sequencing.

Chain terminator sequencing uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. Extension is initiated at a specific site on the template DNA by using a short radioactive, or other labeled, oligonucleotide primer complementary to the template at that region. The oligonucleotide primer is extended using a DNA polymerase, standard four deoxynucleotide bases, and a low concentration of one chain terminating nucleotide, most commonly a di-deoxynucleotide. This reaction is repeated in four separate tubes with each of the bases taking turns as the di-deoxynucleotide. Limited incorporation of the chain terminating nucleotide by the DNA polymerase results in a series of related DNA fragments that are terminated only at positions where that particular di-deoxynucleotide is used. For each reaction tube, the fragments are size-separated by electrophoresis in a slab polyacrylamide gel or a capillary tube filled with a viscous polymer. The sequence is determined by reading which lane produces a visualized mark from the labeled primer as you scan from the top of the gel to the bottom.

Dye terminator sequencing alternatively labels the terminators. Complete sequencing can be performed in a single reaction by labeling each of the di-deoxynucleotide chain-terminators with a separate fluorescent dye, which fluoresces at a different wavelength.

A variety of nucleic acid sequencing methods are contemplated for use in the methods of the present disclosure including, for example, chain terminator (Sanger) sequencing, dye terminator sequencing, and high-throughput sequencing methods. Many of these sequencing methods are well known in the art. See, e.g., Sanger et al., Proc. Natl. Acad. Sci. USA 74:5463-5467 (1997); Maxam et al., Proc. Natl. Acad. Sci. USA 74:560-564 (1977); Drmanac, et al., Nat. Biotechnol. 16:54-58 (1998); Kato, Int. J. Clin. Exp. Med. 2:193-202 (2009); Ronaghi et al., Anal. Biochem. 242:84-89 (1996); Margulies et al., Nature 437:376-380 (2005); Ruparel et al., Proc. Natl. Acad. Sci. USA 102:5932-5937 (2005), and Harris et al., Science 320:106-109 (2008); Levene et al., Science 299:682-686 (2003); Korlach et al., Proc. Natl. Acad. Sci. USA 105:1176-1181 (2008); Branton et al., Nat. Biotechnol. 26(10):1146-53 (2008); Eid et al., Science 323:133-138 (2009); each of which is herein incorporated by reference in its entirety.

A number of DNA sequencing techniques are known in the art, including fluorescence-based sequencing methodologies (See, e.g., Birren et al., Genome Analysis: Analyzing DNA, 1, Cold Spring Harbor, N.Y.; herein incorporated by reference in its entirety). In some embodiments, automated sequencing techniques understood in that art are utilized. In some embodiments, parallel sequencing of partitioned amplicons (PCT Publication No: WO2006084132 to Kevin McKernan et al., herein incorporated by reference in its entirety) is utilized. In some embodiments, bridge amplification (see, e.g., WO 2000/018957, U.S. Pat. Nos. 7,972,820; 7,790,418 and Adessi et al., Nucleic Acids Research (2000): 28(20): E87; each of which are herein incorporated by reference) is utilized. In some embodiments, DNA sequencing by parallel oligonucleotide extension (See, e.g., U.S. Pat. No. 5,750,341 to Macevicz et al., and U.S. Pat. No. 6,306,597 to Macevicz et al., both of which are herein incorporated by reference in their entireties) is utilized. Additional examples of sequencing techniques include the Church polony technology (Mitra et al., 2003, Analytical Biochemistry 320, 55-65; Shendure et al., 2005 Science 309, 1728-1732; U.S. Pat. No. 6,432,360, U.S. Pat. No. 6,485,944, U.S. Pat. No. 6,511,803; herein incorporated by reference in their entireties), the 454 picotiter pyrosequencing technology (Margulies et al., 2005 Nature 437, 376-380; US 20050130173; herein incorporated by reference in their entireties), the Solexa single base addition technology (Bennett et al., 2005, Pharmacogenomics, 6, 373-382; U.S. Pat. No. 6,787,308; U.S. Pat. No. 6,833,246; herein incorporated by reference in their entireties), the Lynx massively parallel signature sequencing technology (Brenner et al. (2000). Nat. Biotechnol. 18:630-634; U.S. Pat. No. 5,695,934; U.S. Pat. No. 5,714,330; herein incorporated by reference in their entireties), and the Adessi PCR colony technology (Adessi et al. (2000). Nucleic Acid Res. 28, E87; WO 00018957; herein incorporated by reference in its entirety).

Next-generation sequencing (NGS) methods share the common feature of massively parallel, high-throughput strategies, with the goal of lower costs in comparison to older sequencing methods (see, e.g., Voelkerding et al., Clinical Chem., 55: 641-658, 2009; MacLean et al., Nature Rev. Microbiol., 7: 287-296; each herein incorporated by reference in their entirety). NGS methods can be broadly divided into those that typically use template amplification and those that do not. Amplification-requiring methods include pyrosequencing commercialized by Roche as the 454 technology platforms (e.g., GS 20 and GS FLX), the Solexa platform commercialized by Illumina, and the Supported Oligonucleotide Ligation and Detection (SOLiD) platform commercialized by Applied Biosystems. Non-amplification approaches, also known as single-molecule sequencing, are exemplified by the HeliScope platform commercialized by Helicos BioSciences, and emerging platforms commercialized by VisiGen, Oxford Nanopore Technologies Ltd., Life Technologies/Ion Torrent, and Pacific Biosciences, respectively.

2. Hybridization

Illustrative non-limiting examples of nucleic acid hybridization techniques include, but are not limited to, in situ hybridization (ISH), microarray, and Southern or Northern blot. In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA or RNA strand as a probe to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough, the entire tissue (whole mount ISH). DNA ISH can be used to determine the structure of chromosomes. RNA ISH is used to measure and localize mRNAs and other transcripts (e.g., pseudogenes) within tissue sections or whole mounts. Sample cells and tissues are usually treated to fix the target transcripts in place and to increase access of the probe. The probe hybridizes to the target sequence at elevated temperature, and then the excess probe is washed away. The probe that was labeled with either radio-, fluorescent- or antigen-labeled bases is localized and quantitated in the tissue using either autoradiography, fluorescence microscopy or immunohistochemistry, respectively. ISH can also use two or more probes, labeled with radioactivity or the other non-radioactive labels, to simultaneously detect two or more transcripts.

In some embodiments, pseudogenes are detected using fluorescence in situ hybridization (FISH). In some embodiments, FISH assays utilize bacterial artificial chromosomes (BACs). These have been used extensively in the human genome sequencing project (see Nature 409: 953-958 (2001)) and clones containing specific BACs are available through distributors that can be located through many sources, e.g., NCBI. Each BAC clone from the human genome has been given a reference name that unambiguously identifies it. These names can be used to find a corresponding GenBank sequence and to order copies of the clone from a distributor.

The present invention further provides a method of performing a FISH assay on human prostate cells, human prostate tissue or on the fluid surrounding said human prostate cells or human prostate tissue. Specific protocols are well known in the art and can be readily adapted for the present invention. Guidance regarding methodology may be obtained from many references including: In situ Hybridization: Medical Applications (eds. G. R. Coulton and J. de Belleroche), Kluwer Academic Publishers, Boston (1992); In situ Hybridization: In Neurobiology; Advances in Methodology (eds. J. H. Eberwine, K. L. Valentino, and J. D. Barchas), Oxford University Press Inc., England (1994); In situ Hybridization: A Practical Approach (ed. D. G. Wilkinson), Oxford University Press Inc., England (1992)); Kuo, et al., Am. J. Hum. Genet. 49:112-119 (1991); Klinger, et al., Am. J. Hum. Genet. 51:55-65 (1992); and Ward, et al., Am. J. Hum. Genet. 52:854-865 (1993)). There are also kits that are commercially available and that provide protocols for performing FISH assays (available from e.g., Oncor, Inc., Gaithersburg, Md.). Patents providing guidance on methodology include U.S. Pat. Nos. 5,225,326; 5,545,524; 6,121,489 and 6,573,043. All of these references are hereby incorporated by reference in their entirety and may be used along with similar references in the art and with the information provided in the Examples section herein to establish procedural steps convenient for a particular laboratory.

3. Microarrays

Different kinds of biological assays are called microarrays including, but not limited to: DNA microarrays (e.g., cDNA microarrays and oligonucleotide microarrays); protein microarrays; tissue microarrays; transfection or cell microarrays; chemical compound microarrays; and, antibody microarrays. A DNA microarray, commonly known as gene chip, DNA chip, or biochip, is a collection of microscopic DNA spots attached to a solid surface (e.g., glass, plastic or silicon chip) forming an array for the purpose of expression profiling or monitoring expression levels for thousands of genes simultaneously. The affixed DNA segments are known as probes, thousands of which can be used in a single DNA microarray. Microarrays can be used to identify disease genes or transcripts (e.g., pseudogenes) by comparing gene expression in disease and normal cells. Microarrays can be fabricated using a variety of technologies, including but not limiting: printing with fine-pointed pins onto glass slides; photolithography using pre-made masks; photolithography using dynamic micromirror devices; ink jet printing; or, electrochemistry on microelectrode arrays.

Southern and Northern blotting is used to detect specific DNA or RNA sequences, respectively. DNA or RNA extracted from a sample is fragmented, electrophoretically separated on a matrix gel, and transferred to a membrane filter. The filter bound DNA or RNA is subject to hybridization with a labeled probe complementary to the sequence of interest. Hybridized probe bound to the filter is detected. A variant of the procedure is the reverse Northern blot, in which the substrate nucleic acid that is affixed to the membrane is a collection of isolated DNA fragments and the probe is RNA extracted from a tissue and labeled.

3. Amplification

Nucleic acids (e.g., pseudogenes) may be amplified prior to or simultaneous with detection. Illustrative non-limiting examples of nucleic acid amplification techniques include, but are not limited to, polymerase chain reaction (PCR), reverse transcription polymerase chain reaction (RT-PCR), transcription-mediated amplification (TMA), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence based amplification (NASBA). Those of ordinary skill in the art will recognize that certain amplification techniques (e.g., PCR) require that RNA be reversed transcribed to DNA prior to amplification (e.g., RT-PCR), whereas other amplification techniques directly amplify RNA (e.g., TMA and NASBA).

The polymerase chain reaction (U.S. Pat. Nos. 4,683,195, 4,683,202, 4,800,159 and 4,965,188, each of which is herein incorporated by reference in its entirety), commonly referred to as PCR, uses multiple cycles of denaturation, annealing of primer pairs to opposite strands, and primer extension to exponentially increase copy numbers of a target nucleic acid sequence. In a variation called RT-PCR, reverse transcriptase (RT) is used to make a complementary DNA (cDNA) from mRNA, and the cDNA is then amplified by PCR to produce multiple copies of DNA. For other various permutations of PCR see, e.g., U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159; Mullis et al., Meth. Enzymol. 155: 335 (1987); and, Murakawa et al., DNA 7: 287 (1988), each of which is herein incorporated by reference in its entirety.

Transcription mediated amplification (U.S. Pat. Nos. 5,480,784 and 5,399,491, each of which is herein incorporated by reference in its entirety), commonly referred to as TMA, synthesizes multiple copies of a target nucleic acid sequence autocatalytically under conditions of substantially constant temperature, ionic strength, and pH in which multiple RNA copies of the target sequence autocatalytically generate additional copies. See, e.g., U.S. Pat. Nos. 5,399,491 and 5,824,518, each of which is herein incorporated by reference in its entirety. In a variation described in U.S. Publ. No. 20060046265 (herein incorporated by reference in its entirety), TMA optionally incorporates the use of blocking moieties, terminating moieties, and other modifying moieties to improve TMA process sensitivity and accuracy.

The ligase chain reaction (Weiss, R., Science 254: 1292 (1991), herein incorporated by reference in its entirety), commonly referred to as LCR, uses two sets of complementary DNA oligonucleotides that hybridize to adjacent regions of the target nucleic acid. The DNA oligonucleotides are covalently linked by a DNA ligase in repeated cycles of thermal denaturation, hybridization and ligation to produce a detectable double-stranded ligated oligonucleotide product. Strand displacement amplification (Walker, G. et al., Proc. Natl. Acad. Sci. USA 89: 392-396 (1992); U.S. Pat. Nos. 5,270,184 and 5,455,166, each of which is herein incorporated by reference in its entirety), commonly referred to as SDA, uses cycles of annealing pairs of primer sequences to opposite strands of a target sequence, primer extension in the presence of a dNTPαS to produce a duplex hemiphosphorothioated primer extension product, endonuclease-mediated nicking of a hemimodified restriction endonuclease recognition site, and polymerase-mediated primer extension from the 3′ end of the nick to displace an existing strand and produce a strand for the next round of primer annealing, nicking and strand displacement, resulting in geometric amplification of product. Thermophilic SDA (tSDA) uses thermophilic endonucleases and polymerases at higher temperatures in essentially the same method (EP Pat. No. 0 684 315).

Other amplification methods include, for example: nucleic acid sequence based amplification (U.S. Pat. No. 5,130,238, herein incorporated by reference in its entirety), commonly referred to as NASBA; one that uses an RNA replicase to amplify the probe molecule itself (Lizardi et al., BioTechnol. 6: 1197 (1988), herein incorporated by reference in its entirety), commonly referred to as Qβ replicase; a transcription based amplification method (Kwoh et al., Proc. Natl. Acad. Sci. USA 86:1173 (1989)); and, self-sustained sequence replication (Guatelli et al., Proc. Natl. Acad. Sci. USA 87: 1874 (1990), each of which is herein incorporated by reference in its entirety). For further discussion of known amplification methods see Persing, David H., “In Vitro Nucleic Acid Amplification Techniques” in Diagnostic Medical Microbiology: Principles and Applications (Persing et al., Eds.), pp. 51-87 (American Society for Microbiology, Washington, D.C. (1993)).

4. Detection Methods

Non-amplified or amplified nucleic acids can be detected by any conventional means. For example, the pseudogenes can be detected by hybridization with a detectably labeled probe and measurement of the resulting hybrids. Illustrative non-limiting examples of detection methods are described below.

One illustrative detection method, the Hybridization Protection Assay (HPA) involves hybridizing a chemiluminescent oligonucleotide probe (e.g., an acridinium ester-labeled (AE) probe) to the target sequence, selectively hydrolyzing the chemiluminescent label present on unhybridized probe, and measuring the chemiluminescence produced from the remaining probe in a luminometer. See, e.g., U.S. Pat. No. 5,283,174 and Norman C. Nelson et al., Nonisotopic Probing, Blotting, and Sequencing, ch. 17 (Larry J. Kricka ed., 2d ed. 1995, each of which is herein incorporated by reference in its entirety).

Another illustrative detection method provides for quantitative evaluation of the amplification process in real-time. Evaluation of an amplification process in “real-time” involves determining the amount of amplicon in the reaction mixture either continuously or periodically during the amplification reaction, and using the determined values to calculate the amount of target sequence initially present in the sample. A variety of methods for determining the amount of initial target sequence present in a sample based on real-time amplification are well known in the art. These include methods disclosed in U.S. Pat. Nos. 6,303,305 and 6,541,205, each of which is herein incorporated by reference in its entirety. Another method for determining the quantity of target sequence initially present in a sample, but which is not based on a real-time amplification, is disclosed in U.S. Pat. No. 5,710,029, herein incorporated by reference in its entirety.

Amplification products may be detected in real-time through the use of various self-hybridizing probes, most of which have a stem-loop structure. Such self-hybridizing probes are labeled so that they emit differently detectable signals, depending on whether the probes are in a self-hybridized state or an altered state through hybridization to a target sequence. By way of non-limiting example, “molecular torches” are a type of self-hybridizing probe that includes distinct regions of self-complementarity (referred to as “the target binding domain” and “the target closing domain”) which are connected by a joining region (e.g., non-nucleotide linker) and which hybridize to each other under predetermined hybridization assay conditions. In a preferred embodiment, molecular torches contain single-stranded base regions in the target binding domain that are from 1 to about 20 bases in length and are accessible for hybridization to a target sequence present in an amplification reaction under strand displacement conditions. Under strand displacement conditions, hybridization of the two complementary regions, which may be fully or partially complementary, of the molecular torch is favored, except in the presence of the target sequence, which will bind to the single-stranded region present in the target binding domain and displace all or a portion of the target closing domain. The target binding domain and the target closing domain of a molecular torch include a detectable label or a pair of interacting labels (e.g., luminescent/quencher) positioned so that a different signal is produced when the molecular torch is self-hybridized than when the molecular torch is hybridized to the target sequence, thereby permitting detection of probe:target duplexes in a test sample in the presence of unhybridized molecular torches. Molecular torches and a variety of types of interacting label pairs are disclosed in U.S. Pat. No. 6,534,274, herein incorporated by reference in its entirety.

Another example of a detection probe having self-complementarity is a “molecular beacon.” Molecular beacons include nucleic acid molecules having a target complementary sequence, an affinity pair (or nucleic acid arms) holding the probe in a closed conformation in the absence of a target sequence present in an amplification reaction, and a label pair that interacts when the probe is in a closed conformation. Hybridization of the target sequence and the target complementary sequence separates the members of the affinity pair, thereby shifting the probe to an open conformation. The shift to the open conformation is detectable due to reduced interaction of the label pair, which may be, for example, a fluorophore and a quencher (e.g., DABCYL and EDANS). Molecular beacons are disclosed in U.S. Pat. Nos. 5,925,517 and 6,150,097, herein incorporated by reference in its entirety.

Other self-hybridizing probes are well known to those of ordinary skill in the art. By way of non-limiting example, probe binding pairs having interacting labels, such as those disclosed in U.S. Pat. No. 5,928,862 (herein incorporated by reference in its entirety) might be adapted for use in the present invention. Probe systems used to detect single nucleotide polymorphisms (SNPs) might also be utilized in the present invention. Additional detection systems include “molecular switches,” as disclosed in U.S. Publ. No. 20050042638, herein incorporated by reference in its entirety. Other probes, such as those comprising intercalating dyes and/or fluorochromes, are also useful for detection of amplification products in the present invention. See, e.g., U.S. Pat. No. 5,814,447 (herein incorporated by reference in its entirety).

ii. Data Analysis

In some embodiments, a computer-based analysis program is used to translate the raw data generated by the detection assay (e.g., the presence, absence, or amount of a given marker or markers) into data of predictive value for a clinician. The clinician can access the predictive data using any suitable means. Thus, in some preferred embodiments, the present invention provides the further benefit that the clinician, who is not likely to be trained in genetics or molecular biology, need not understand the raw data. The data is presented directly to the clinician in its most useful form. The clinician is then able to immediately utilize the information in order to optimize the care of the subject.

The present invention contemplates any method capable of receiving, processing, and transmitting the information to and from laboratories conducting the assays, information provides, medical personal, and subjects. For example, in some embodiments of the present invention, a sample (e.g., a biopsy or a serum or urine sample) is obtained from a subject and submitted to a profiling service (e.g., clinical lab at a medical facility, genomic profiling business, etc.), located in any part of the world (e.g., in a country different than the country where the subject resides or where the information is ultimately used) to generate raw data. Where the sample comprises a tissue or other biological sample, the subject may visit a medical center to have the sample obtained and sent to the profiling center, or subjects may collect the sample themselves (e.g., a urine sample) and directly send it to a profiling center. Where the sample comprises previously determined biological information, the information may be directly sent to the profiling service by the subject (e.g., an information card containing the information may be scanned by a computer and the data transmitted to a computer of the profiling center using an electronic communication systems). Once received by the profiling service, the sample is processed and a profile is produced (i.e., expression data), specific for the diagnostic or prognostic information desired for the subject.

The profile data is then prepared in a format suitable for interpretation by a treating clinician. For example, rather than providing raw expression data, the prepared format may represent a diagnosis or risk assessment (e.g., presence or absence of a pseudogene) for the subject, along with recommendations for particular treatment options. The data may be displayed to the clinician by any suitable method. For example, in some embodiments, the profiling service generates a report that can be printed for the clinician (e.g., at the point of care) or displayed to the clinician on a computer monitor.

In some embodiments, the information is first analyzed at the point of care or at a regional facility. The raw data is then sent to a central processing facility for further analysis and/or to convert the raw data to information useful for a clinician or patient. The central processing facility provides the advantage of privacy (all data is stored in a central facility with uniform security protocols), speed, and uniformity of data analysis. The central processing facility can then control the fate of the data following treatment of the subject. For example, using an electronic communication system, the central facility can provide data to the clinician, the subject, or researchers.

In some embodiments, the subject is able to directly access the data using the electronic communication system. The subject may chose further intervention or counseling based on the results. In some embodiments, the data is used for research use. For example, the data may be used to further optimize the inclusion or elimination of markers as useful indicators of a particular condition or stage of disease or as a companion diagnostic to determine a treatment course of action.

iii. In Vivo Imaging

Pseudogenes (e.g., ATP8A2-Ψ, DPP3, CXADR-Ψ, NDUFA9, EPCAM, PDAP1, RBM17, CES7 and KLK4-KLKP1) may also be detected using in vivo imaging techniques, including but not limited to: radionuclide imaging; positron emission tomography (PET); computerized axial tomography, X-ray or magnetic resonance imaging method, fluorescence detection, and chemiluminescent detection. In some embodiments, in vivo imaging techniques are used to visualize the presence of or expression of cancer markers in an animal (e.g., a human or non-human mammal). For example, in some embodiments, cancer marker mRNA or protein is labeled using a labeled antibody specific for the cancer marker. A specifically bound and labeled antibody can be detected in an individual using an in vivo imaging method, including, but not limited to, radionuclide imaging, positron emission tomography, computerized axial tomography, X-ray or magnetic resonance imaging method, fluorescence detection, and chemiluminescent detection. Methods for generating antibodies to the cancer markers of the present invention are described below.

The in vivo imaging methods of embodiments of the present invention are useful in the identification of cancers that express pseudogenes (e.g., prostate cancer). In vivo imaging is used to visualize the presence or level of expression of a pseudogene. Such techniques allow for diagnosis without the use of an unpleasant biopsy. The in vivo imaging methods of embodiments of the present invention can further be used to detect metastatic cancers in other parts of the body.

In some embodiments, reagents (e.g., antibodies) specific for the cancer markers of the present invention are fluorescently labeled. The labeled antibodies are introduced into a subject (e.g., orally or parenterally). Fluorescently labeled antibodies are detected using any suitable method (e.g., using the apparatus described in U.S. Pat. No. 6,198,107, herein incorporated by reference).

In other embodiments, antibodies are radioactively labeled. The use of antibodies for in vivo diagnosis is well known in the art. Sumerdon et al., (Nucl. Med. Biol 17:247-254 [1990] have described an optimized antibody-chelator for the radioimmunoscintographic imaging of tumors using Indium-111 as the label. Griffin et al., (J Clin Onc 9:631-640 [1991]) have described the use of this agent in detecting tumors in patients suspected of having recurrent colorectal cancer. The use of similar agents with paramagnetic ions as labels for magnetic resonance imaging is known in the art (Lauffer, Magnetic Resonance in Medicine 22:339-342 [1991]). The label used will depend on the imaging modality chosen. Radioactive labels such as Indium-111, Technetium-99m, or Iodine-131 can be used for planar scans or single photon emission computed tomography (SPECT). Positron emitting labels such as Fluorine-19 can also be used for positron emission tomography (PET). For MRI, paramagnetic ions such as Gadolinium (III) or Manganese (II) can be used.

Radioactive metals with half-lives ranging from 1 hour to 3.5 days are available for conjugation to antibodies, such as scandium-47 (3.5 days) gallium-67 (2.8 days), gallium-68 (68 minutes), technetiium-99m (6 hours), and indium-111 (3.2 days), of which gallium-67, technetium-99m, and indium-111 are preferable for gamma camera imaging, gallium-68 is preferable for positron emission tomography.

A useful method of labeling antibodies with such radiometals is by means of a bifunctional chelating agent, such as diethylenetriaminepentaacetic acid (DTPA), as described, for example, by Khaw et al. (Science 209:295 [1980]) for In-111 and Tc-99m, and by Scheinberg et al. (Science 215:1511 [1982]). Other chelating agents may also be used, but the 1-(p-carboxymethoxybenzyl) EDTA and the carboxycarbonic anhydride of DTPA are advantageous because their use permits conjugation without affecting the antibody's immunoreactivity substantially.

Another method for coupling DPTA to proteins is by use of the cyclic anhydride of DTPA, as described by Hnatowich et al. (Int. J. Appl. Radiat. Isot. 33:327 [1982]) for labeling of albumin with In-111, but which can be adapted for labeling of antibodies. A suitable method of labeling antibodies with Tc-99m which does not use chelation with DPTA is the pretinning method of Crockford et al., (U.S. Pat. No. 4,323,546, herein incorporated by reference).

A method of labeling immunoglobulins with Tc-99m is that described by Wong et al. (Int. J. Appl. Radiat. Isot., 29:251 [1978]) for plasma protein, and recently applied successfully by Wong et al. (J. Nucl. Med., 23:229 [1981]) for labeling antibodies.

In the case of the radiometals conjugated to the specific antibody, it is likewise desirable to introduce as high a proportion of the radiolabel as possible into the antibody molecule without destroying its immunospecificity. A further improvement may be achieved by effecting radiolabeling in the presence of the pseudogene, to insure that the antigen binding site on the antibody will be protected. The antigen is separated after labeling.

In still further embodiments, in vivo biophotonic imaging (Xenogen, Almeda, Calif.) is utilized for in vivo imaging. This real-time in vivo imaging utilizes luciferase. The luciferase gene is incorporated into cells, microorganisms, and animals (e.g., as a fusion protein with a cancer marker of the present invention). When active, it leads to a reaction that emits light. A CCD camera and software is used to capture the image and analyze it.

iv. Compositions & Kits

Compositions for use in the diagnostic methods described herein include, but are not limited to, probes, amplification oligonucleotides, and the like. In some embodiments, kits include all components necessary, sufficient or useful for detecting the markers described herein (e.g., reagents, controls, instructions, etc.). The kits described herein find use in research, therapeutic, screening, and clinical applications.

The probe and antibody compositions of the present invention may also be provided in the form of an array.

II. Drug Screening Applications

In some embodiments, the present invention provides drug screening assays (e.g., to screen for anticancer drugs). The screening methods of the present invention utilize pseudogenes. For example, in some embodiments, the present invention provides methods of screening for compounds that alter (e.g., decrease) the expression or activity of pseudogenes. The compounds or agents may interfere with transcription, by interacting, for example, with the promoter region. The compounds or agents may interfere with mRNA (e.g., by RNA interference, antisense technologies, etc.). The compounds or agents may interfere with pathways that are upstream or downstream of the biological activity of pseudogenes. In some embodiments, candidate compounds are antisense or interfering RNA agents (e.g., oligonucleotides) directed against pseudogenes. In other embodiments, candidate compounds are antibodies or small molecules that specifically bind to a pseudogenes regulator or expression products inhibit its biological function.

In one screening method, candidate compounds are evaluated for their ability to alter pseudogenes expression by contacting a compound with a cell expressing a pseudogene and then assaying for the effect of the candidate compounds on expression. In some embodiments, the effect of candidate compounds on expression of pseudogenes is assayed for by detecting the level of pseudogene expressed by the cell. mRNA expression can be detected by any suitable method.

EXPERIMENTAL

The following examples are provided in order to demonstrate and further illustrate certain preferred embodiments and aspects of the present invention and are not to be construed as limiting the scope thereof.

Example 1 A. Methods Dataset

Paired end transcriptome sequence reads (2×40 and 2×80 base pairs) were obtained from 13 tissue types including breast, prostate, pancreas, gastric, melanoma, and other tissues comprising a total of over 293 individual samples (FIG. 7, Table 1). Each sample was sequenced on an Illumina Genome Analyzer I or II according to protocols provided by Illumina, described earlier (Maher et al., 2009b Proceedings of the National Academy of Sciences of the United States of America 106, 12353-12358).

Pseudogene Analysis Pipeline

Paired end transcriptome reads were mapped to the human genome (NCBI36/hg18) and University of California Santa Cruz (UCSC) Genes using Efficient Alignment of Nucleotide Databases (ELAND) software of the Illumina Genome Analyzer Pipeline, using 32 bp seed length, allowing up to 2 mismatches; detailed mapping status are represented in Table 2. Table 2 shows primary mapping status of individual sequencing lanes. Flowcell and lane ID (Column A), total number of reads (Column B), purity filter reads (Column C), followed by mapping count for each chromosome (hs_ref_chr1-22, X, and Y) including mitochondrial (chrM) and ribosomal sequences (humRibosomal) (Column D-AC). Passed purity filter reads obtained from Illumina export and extended output files (as described before) were parsed and binned into three major categories: 1. Both of the paired reads map to annotated genes 2. One or both of the paired reads map to un-annotated regions in the genome, and 3. Neither of the reads map (these include viral, bacterial, and other contaminant reads, as well as sequencing errors). The paired reads with one or both partners mapping to an un-annotated region were clustered based on overlaps of aligned sequences using the chromosomal coordinates of the clusters. Singleton reads that did not cluster or stacked\duplicated reads with same start and stop genomic-coordinates (potential PCR artifacts) were filtered out. Passed filter ‘clusters’ were defined as units of transcript expression (analogous to a ‘probe’ on microarray platforms). These ‘clusters’ were screened against publicly available human pseudogene resources, Yale human pseudogene Build 53-processed, duplicate and fragment entries (Karro et al., 2007 Nucleic acids research 35, D55-60) and Gencode Manual Gene Annotations (level 1+2), Automated Gene Annotations (level 3) (October 2009) (Zheng et al., 2007 Genome research 17, 839-851) to identify and annotate pseudogene ‘clusters’. The clusters were also subjected to homology search using the alignment tool BLAT (Kent, 2002 Genome research 12, 656-664) for an independent annotation. Sequence reads from individual samples were queried against the resultant clusters defined by the union of Yale, ENCODE and BLAT output to assess the expression of pseudogenes (FIG. 1). A stringent cutoff value for pseudogene expression in a sample was set at five or more reads mapping to at least one cluster in a putative pseudogene transcript.

Data from individual samples was used to construct a matrix to carry out pseudogene expression profiling. Pseudogene transcripts (one or more probe(s) overlapping with either Yale or ENCODE) in 2 or more samples in a tissue type and its absence in all other tissue types was used to define it as tissue specific. If a pseudogene probe was detected in 10 out of 13 samples, it was designated as ubiquitous. All other cases were described as intermediate category. Pseudogene transcripts detected in 3 or more cancer samples and absent in all benign samples were assigned as cancer specific.

RNA Isolation and cDNA Synthesis

Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) with DNase I digestion according to the manufacturer's instructions. RNA integrity was verified on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, Calif.). cDNA was synthesized from total RNA using Superscript III (Invitrogen) and random primers (Invitrogen).

Quantitative Real-Time PCR

Quantitative Real-time PCR (qPCR) was performed using Taqman or SYBR green based assays (Applied Biosystems, Foster City, Calif.) on an Applied Biosystems 7900HT Real-Time PCR System, according to standard protocols. The Taqman assays for CXADR and ATP8A2 assays were custom designed based on regions of differences between the wild type and pseudogene sequences. Oligonucleotide primers for SYBR green assays were obtained from Integrated DNA Technologies (Coralville, Iowa). The housekeeping gene, GAPDH, was used as a loading control. Fold changes were calculated relative to GAPDH and normalized to the median value of the benign samples.

(SEQ ID NO: 1) CXADR-Ψ_F CGGTTTCAGTGCTCTATGTTGTTTG (SEQ ID NO: 2) CXADR-Ψ_R TAAATTTAGGATTACATGTTTCTAGAACA (SEQ ID NO: 3) CXADR-Ψ_M 6FAM ATGCCATCCAAAACCA (SEQ ID NO: 4) ATP8A2-Ψ_F CTGGTGTTCTTTGGCATCTACTCA (SEQ ID NO: 5) ATP8A2-Ψ_R CAGCTCAGGATCACAGTTGCT (SEQ ID NO: 6) ATP8A2-Ψ_M 6FAM CTGGTCCACCATTCTC (SEQ ID NO: 7) ATP8A2-WT_F ATCCTATTGAAGGAGGACTCTTTGGA (SEQ ID NO: 8) ATP8A2-WT_R CCAGCAAATTCCCAAGGTCAGT (SEQ ID NO: 9) ATP8A2-WT_M 6FAM AAGGGCAGCCATTACT (SEQ ID NO: 10) KLK4-KLKP1_F ATGGAAAACGAATTGTTCTG (SEQ ID NO: 11) KLK4-KLKP1_R CAGTGTTCCGGGTGATGCAG Additionally, inventoried Taqman assay for CXADR-WT (Hs00154661_m1) and ATP8A2-WT (assay ID hs00185259_m1) were used.

B. Results

Development of a Bioinformatics Platform for the Analysis of Pseudogene Transcription

High throughput transcriptome sequencing always yields a fraction of reads that do not map perfectly to the reference genome/transcriptome. This sequence fraction has been actively mined for aberrant transcripts including mutations (Shah et al., 2009a N Engl J Med 360, 2719-2729; Shah et al., 2009b Nature 461, 809-813; Tuch et al. PloS one 5, e9317), chimeric RNAs (Maher et al., 2009a Nature 458, 97-101; Maher et al., 2009b Proceedings of the National Academy of Sciences of the United States of America 106, 12353-12358), xenobiotic sequences, and non-coding RNAs (Gupta et al. Nature 464, 1071-1076; Loewer et al. Nature genetics 42, 1113-1117; Wilhelm et al., 2008 Nature 453, 1239-1243). In this study the sequencing reads that showed a highdegree of homology but imperfect match to the reference genes, but mapped perfectly elsewhere in the genome, were used to serve as the primary data for pseudogene expression analysis (FIG. 1). Thus, paired-end RNA-Seq data from a compendium of 293 samples, representing both cancer and benign samples from 13 different tissue types was utilized to build the pseudogene analysis pipeline (FIG. 7, Table 1). Sequencing reads were mapped to the human genome (hg18) and University of California Santa Cruz (UCSC) Genes using Efficient Alignment of Nucleotide Databases (ELAND) software of the Illumina Genome Analyzer Pipeline. Reads that contained three or more mismatches to the reference genes but mapped perfectly to un-annotated regions, elsewhere in the genome, were used to generate de novo ‘clusters’ (that ranged from 40 to 5000 bps). All the clusters that contained two or more unique, high quality overlapping reads—nucleating at the loci of differences between wild type genes and pseudogenes were retained for further analysis of pseudogene transcripts (FIG. 1). The clusters were employed for gene expression analyses in a way analogous to the ‘probes’ used in microarray gene expression studies; albeit, unlike predesigned and fixed probes used in microarrays, the sequence clusters used here were formed de novo, solely based on the presence (and levels) of transcripts. Thus one or more clusters (like one or more probes in microarrays) represented a transcript, while the number of reads mapping to a cluster (analogous to fluorescence intensity due to probe hybridization on microarrays) provided a measure of expression of the corresponding genes. For example, FIG. 2 shows a schematic representation of the cluster alignments for two representative pseudogenes, ATP8A2-Ψ (top) and CXADR-Ψ (bottom), and as seen in the figure, mutation-dense regions in the transcripts provide loci of cluster formation.

Overall, 2156 unique clusters were defined in terms of their genomic coordinates (start and end points) that were compared against annotated pseudogenes in the ENCODE and the Yale Gerstein Group (referred to as Yale) (Kano et al., 2007 Nucleic acids research 35, D55-60) databases, the two most comprehensive pseudogene annotation resources. Of the 2156 initial clusters, 934 overlapped with both the Yale and ENCODE databases, whereas 81 were found only in the Yale database and 15 only in the ENCODE database, overall accounting for 1506 distinct pseudogene transcripts corresponding to 1000 unique genes (FIG. 8). Further, because the RNASeq compendium is comprised of 35-45 mer short sequence reads that largely generated short sequence clusters not optimal for pseudogene analysis tools such as Pseudopipe (Zhang et al., 2006 Bioinformatics (Oxford, England) 22, 1437-1439) and Pseudofam (Lam et al., 2009 Nucleic acids research 37, D738-743) used in generating ENCODE and Yale databases, we also carried out a direct query of individual clusters against the human genome (hg18) using the BLAT tool from UCSC, that is ideally suited for short sequence alignment searches (Kent, 2002). Using this BLAT analysis, also referred as the “custom” analysis (FIG. 8A), it was possible to independently assign 1888 clusters representing 1820 unique pseudogenes to a unique genomic location. Comparing the genomic locations of the pseudogene clusters identified by BLAT analysis to those identified by Yale and ENCODE databases (FIG. 8A), 762 clusters were found to be common to all the three resources, but a large set of 585 clusters were uniquely identified by BLAT analysis.

Some clusters were seen to be localized in the vicinity of known pseudogenes. 92 clusters that resided adjacent (within 5 kb) to previously annotated pseudogenes (FIG. 8B, left) were identified. It was hypothesized that these represent pseudogenes with inaccurate annotations in the current databases. For example, the chromosomal coordinates of CENTG2-Ψ (OTTHUMT00000085288, Havana processed pseudogene) are defined in ENCODE as Chr1:177822463-177824935. A cluster mapping to this locus was observed; a distinct cluster (Chr1:177825028-177826295) less than 100 base pairs away was also observed. Although un-annotated in the current databases, the sequence of this adjacent locus shows a high degree of homology to the CENTG2 parental gene (FIG. 8B, right), indicating that the novel cluster represents an extension of the existing genomic coordinates of CENTG2-Ψ annotation. Similar observations were made with HNRNPA1 and the HNRNPA1-Ψ on Chr6q27 (FIG. 8B, right). The majority of clusters in close proximity to annotated pseudogenes however, did not follow this pattern, and these likely represent putative novel pseudogenes currently missing in the database annotations. Overall, the pseudogene clusters common to the Yale, ENCODE and ‘custom’ datasets, as well as those common to any two of these subsets, were identified as representing ‘expressed pseudogenes’, that were taken up for further analyses.

Further, taking into account the instances of multiple clusters representing the same pseudogene transcript, the 2156 transcript clusters overall amounted to transcriptional evidence of 2082 distinct pseudogenes, of which 1506 transcripts correspond to specific genomic coordinates in Yale and/or ENCODE pseudogenes, and as many as 576 potentially novel transcripts (described below) (FIG. 8A). The 2082 pseudogene transcripts in turn correspond to 1437 wild type genes, clearly indicating that transcription of multiple pseudogenes arisen from the same wild type genes are also detected in our compendium. Taken together, the study provides evidence of widespread transcription of pseudogenes unraveled by high throughput transcriptome sequencing (Table 6A).

A closer look at the coverage of pseudogene clusters across the sample-wise compendium reveals that pseudogenes of housekeeping genes such as ribosomal and proteins are widely expressed across tissue types. Pseudogene transcripts corresponding to ribosomal proteins RPL-1, -3, -5, -6, -8, -9, -10, -11, -13, -18, -22, -23, -27, -28 and RPS-5, -6, -10, -11, -14, -16, -18, -20, -21 etc. were all observed in more than 50 samples each. Apart from housekeeping genes, several of the pseudogenes seen to be widely expressed included CALM2 (calmodulin 2 phosphorylase kinase, delta), TOMM40 (translocase of outer mitochondrial membrane 40), NONO (non-POU domain containing, octamer-binding), DUSP8 (dual specificity phosphatase 8), PERP (TP53 apoptosis effector), YES (v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1) and others, were all found to be expressed in more than 50 of the samples examined by RNA-seq, as well as independently verified by pseudogene specific RT-PCR followed by validation through Sanger sequencing (Table 6A and 7, FIG. 14).

Further, because the RNA-Seq compendium is comprised of 35-45 mer short sequence reads that largely generated short sequence clusters not optimal for pseudogene analysis tools such as Pseudopipe (Zhang et al., 2006, supra) and Pseudofam (Lam et al., 2009, supra) used in generating ENCODE and Yale databases, we also carried out a direct query of individual clusters against the human genome (hg18) using the BLAT tool from UCSC, that is ideally suited for short sequence alignment searches (Kent, 2002 Genome research 12, 656-664). Using this BLAT analysis, also referred as the “custom” analysis or simply BLAT (FIG. 82A), it was possible to independently assign 1888 clusters representing 1820 unique pseudogenes to unique genomic locations. Comparing the genomic locations of the pseudogene clusters identified by BLAT analysis to those identified by Yale and ENCODE databases (FIG. 8A), 762 clusters were found to be common to all the three resources, but a remarkably large set of 585 clusters were uniquely defined by BLAT analysis alone. Some of the novel pseudogene transcripts thus identified including BAT1, BTBD1, COX7A2L, CTNND1, EIF5, PAPOLA, PARP11, SYT, and ZBTB12 and others (n=25) were validated by RT-PCR followed by Sanger sequencing (Table 7). Thus, analysis of RNA-seq data was producing reliable prediction of expressed pseudogenes.

Given the utility of RNA-seq in unraveling pseudogene transcription, the technical and analytical factors influencing the yield of pseudogene transcripts were assesed through transcriptome sequencing. A positive correlation was observed between the sequencing depth and total number of pseudogene transcripts (correlation co-efficient, +0.65) (FIG. 9). On the other hand, no significant correlation was observed between the absolute measure of percent similarity between pseudogene 10 WT pairs and pseudogene yield (FIG. 10). The metric of overall percent similarity accounts for gap penalty and mismatches in BLAT search, but, it is the ‘distribution’ of the mismatches that is critical in resolving pseudogenes from nearly identical wild type sequences—for example, few mismatches, accumulated in a small stretch are more effective in confidently distinguishing pseudogene expression from wild types as compared to higher number of mismatches, but scattered over long stretches of sequence (FIG. 2). Thus, three primary factors determine the detection of pseudogene transcription by RNA-seq 1) the level of expression of the pseudogenes (e.g., the higher the level of expression, higher the likelihood of detection), 2) the depth of RNAsequencing and 3) overall distribution of mismatches with respect to the wild type.

To explore regulatory elements associated with expressed pseudogenes, the pseudogene loci was subjected to two independent promoter analysis tools namely Transfac and Genomatix-Promoter Inspector. These tools provide information only on previously annotated promoter elements associated with known genes and were unable to identify potential promoter elements associated with the pseudogene loci solely based on query sequences. Therefore, ChIP-seq analysis of a breast cancer cell line MCF7 probed with H3K4me3, a histone mark associated with transcriptionally active chromosomal loci, was performed and the results were interogated with the MCF7 pseudogene transcript data. A statistically significant enrichment of H3K4me3 peaks at expressed pseudogene loci as compared to non-expressed pseudogenes (p-value=0.0145) was observed (FIG. S4), indicating that the pseudogene transcripts observed by RNA-seq are associated with transcriptionally active genomic loci. The pseudogene transcripts associated with H3K4Me3 peaks encompass both unprocessed and processed pseudogenes, with no discernible differences in the pattern of expression. Next, the correlation between the expression of pseudogenes present within the introns of unrelated, expressed genes, with their ‘host’ genes was assessed. No significant association was observed, indicating that pseudogenes are likely subject to independent regulatory mechanisms—even when residing within other transcriptionally active genes. Further, the observations with the breast specific unprocessed pseudogene ATP8A2 (likely arisen from duplication of wild type ATP8A2, thus likely harboring similar promoter elements) also indicate that there is no apparent correlation between the pseudogene expression with the wild type gene that is expressed ubiquitously (FIG. 6A, B). Next, the correlation between expression of pseudogenes with that of cognate wild type genes was assessed and no significant pattern of correlation was observed (FIG. 11).

Patterns of Pseudogene Expression in Human Tissues

Next, the expression patterns of the pseudogene transcripts in the RNA-seq compendium comprising of data from 248 cancer and 45 benign samples from 13 different tissue types (total 293 samples) were analyzed. Broad patterns of pseudogene expression, including 1056 pseudogenes that were detected in multiple samples (Table 3) were observed, which supports the hypothesis that transcribed pseudogenes contribute to the typical transcriptional repertoire of cells. In addition, distinct patterns of pseudogene expression, akin to that of protein-coding genes, including 154 highly tissuespecific and 848 moderately tissue-specific (or tissue-enriched) pseudogenes (FIG. 3) were identified. Moreover, 165 pseudogenes exhibiting expression in more than 10 of the 13 tissue types examined were observed, and these were classified as ubiquitous pseudogenes whose transcription is characteristic of most cell types (FIG. 3, bottom).

Of the 165 ubiquitous pseudogenes, a majority belonged to housekeeping genes, such as GAPDH, ribosomal proteins, several cytokeratins, and other genes widely expressed in most cell types. These genes are known to have numerous pseudogenes, and it is likely that several of these pseudogenes retain the capacity for widespread transcription, mimicking their protein-coding counterparts.

A second set of pseudogenes exhibited near-ubiquitous expression, but were frequently transcribed at lower levels in most tissues and robustly transcribed in one or two tissues. These pseudogenes were termed “non-specific”, and this group harbors more than 870 pseudogenes, comprising a large portion of our dataset (FIG. 3, middle). Many of the pseudogenes previously shown to be expressed were found in this category, including some pseudogenes previously reported as tissue specific such as CYP4Z2P, a pseudogene previously reported to be expressed only in breast cancer tissues (Rieger et al., 2004 Cancer research 64, 2357-2364). Other candidates observed in this category include pseudogenes derived from Oct-4 (Kastler et al. The Prostate 70, 666-674), Connexin-43 (Bier et al., 2009 Molecular cancer therapeutics 8, 786-793; Kandouz et al., 2004 Oncogene 23, 4763-4770) and BRAF (Zou et al., 2009 Neoplasia New York, N.Y. 11, 57-65), among others (Table 3).

A notable pseudogene not observed is the recently described PTENP1, a pseudogene of PTEN recently implicated in the biology of the PI-3K signaling pathway (Poliseno et al. Nature 465, 1033-1038). No sequencing reads for PTENP1 were observed in the entire compendium—possibly due to the preponderance of cancer samples in the cohort, which tend to show low expression or deletion of this pseudogene (Poliseno et al. Nature 465, 1033-1038).

Tissue- and Cancer-Specific Pseudogene Expression Signatures

154 pseudogenes with highly specific expression patterns were observed, including pseudogenes derived from AURKA (kidney samples), RHOB (colon samples), and HMGB1 (myeloproliferative neoplasms (MPNs)) (FIG. 3, right). Tissue-specific pseudogenes tended to represent a small fraction of all pseudogenes expressed in a given tissue type, and the total number of tissue-specific pseudogenes observed in a tissue type did not show a correlation with the total number of samples analyzed. For example, B-lymphocyte cells (n=19) and MPNs (n=9) showed more tissue-specific pseudogenes than breast (n=64) or prostate (n=89). More pseudogene transcripts were observed in samples with longer read lengths and deeper coverage. Together, these data both confirm and formalize previous anecdotal observations of tissue-specific pseudogene expression patterns by exploiting the power of RNA-Seq to resolve individual transcripts (FIG. 3, top) (Bier et al., 2009 Molecular cancer therapeutics 8, 786-793; Lu et al., 2006 The Prostate 66, 936-944; Rieger et al., 2004 Cancer research 64, 2357-2364).

Because the sample compendium has a substantial number of cancer samples, pseudogenes with cancer-specific expression were next investigated. While a majority of the pseudogenes examined were found in both cancer and benign samples, 218 pseudogenes were expressed only in cancer samples, of which 178 were observed in multiple cancers and 40 were found to have highly-specific expression in a single cancer type only (FIG. 4; Table 4). The number of cancer-type-specific pseudogenes did not correlate with the number of samples sequenced in a given cancer type. These results indicate that cancer samples harbor transcriptional patterns of pseudogenes that are both lineage- and cancer-specific.

Among the cancer-specific pseudogenes, a few noteworthy examples included pseudogenes derived from the eukaryotic translation initiation factors EIF4A1 and EIF4H, the heterogeneous nuclear ribonucleoprotein HNRPH2, and the small nuclear ribonucleoprotein SNRPG (FIG. 4). Moreover, pseudogenes corresponding to known cancer-associated genes, including RAB-1, a Ras-related protein, VDAC1, a type-1 voltage dependent anion-selective channel/porin, RCC2, a regulator of chromosome condensation 2, and PTMA, prothymosin alpha were observed (FIG. 4). The parental protein-coding PTMA gene has given rise to five processed pseudogenes that retain consensus TATA elements, individual transcriptional start sites, and intact open reading frames that may potentially code for proteins closely related to the parental PTMA protein. Expression of PTMA-derived pseudogenes were found in more than 30 cancer samples, but not in any benign cells (FIG. 4), and these data indicate that PTMA-derived pseudogenes may not only contribute transcripts to cancer cell biology but potentially novel proteins as well.

Breast Cancer Pseudogenes

To investigate individual pseudogenes in greater detail, pseudogenes associated with breast and prostate cancer were investigated. Among the candidates in breast cancer, a novel unprocessed pseudogene cognate to ATP8A2, a LIM domain containing protein speculated to be associated with stress response and proliferative activity (Khoo et al., 1997 Protein expression and purification 9, 379-387), and DPP3, a metallopeptidase shown to have increased activity in endometrial and ovarian cancers (Simaga et al., 2003 Gynecologic oncology 91, 194-200) were investigated (FIG. 3, top; Table 3). Because ATP8A2-Ψ (on chromosome 10) displays substantial sequence divergence from the cognate ATP8A2 parental gene (on chromosome 13) thereby lending high confidence to the computational identification—this candidate was selected for further validation. Taqman assays were designed to distinguish wild type ATP8A2 transcripts from ATP8A2-Ψ and multiple tissue types (including breast, prostate, melanoma, lung, pancreatic cancer, and chronic myeloid leukemia (CML)) were assayed for expression. It was found that ATP8A2-Ψ expression was restricted to breast samples, and that this pseudogene displays profound upregulation in a subset of breast cancer tissues and cell lines (FIG. 5A,B). By contrast, expression of the parental ATP8A2 had no correlation with ATP8A2-Ψ expression and its expression was highly variable across different tissue types in the cohort, with the most pronounced expression intriguingly observed in prostate samples (FIG. 5A, lower panel). As ATP8A2-Ψ is an unprocessed pseudogene and has significant mappable difference with respect to its wild type, a significant correlation (R2=0.98) between the expression pattern obtained by RNA-seq and qPCR values was observed.

Approximately 25% of breast tumors demonstrate extremely high levels of this pseudogene, indicating that ATP8A2-Ψ may contribute to a particular subtype of breast cancer. ATP8A2-Ψexpression with respect to luminal and basal breast subtypes, two prominent categories of breast cancer with distinct molecular and clinical characteristics was analyzed. It was found that ATP8A2-Ψ expression was restricted to tumors with luminal histology, whereas basal tumors showed minimal expression of this pseudogene (FIG. 5B, right). The wild-type ATP8A2 transcript did not display this pattern of expression.

To investigate the role of ATP8A2-Ψ expression in breast cancer, siRNA based knockdown of both the wild type and pseudogene RNA was pereformed in two independent breast cancer cell lines that expressed both the transcripts (FIG. 15A). Knockdown of ATP8A2-Ψ, with two independent siRNAs was found to specifically inhibit the proliferation of overexpressing cell lines Cama1 and HCC1806 (FIG. 6C) but not the cell lines with no detectable levels of ATP8A2-Ψ for example, the benign breast epithelial cell line, H16N2 (FIG. 6C, right) and a pancreatic cancer cell line, BXPC3 (FIG. 15D). Knockdown of ATP8A2-Ψ but not ATP8A2-WT also resulted in reduced cell migration and invasion seen in in vitro Boyden Chamber assays (FIG. 6D) as well as in in vivo intravasation and metastasis in chicken chorioallantoic membrane xenograft assay (FIG. 6F). In contrast, knockdown of wild type ATP8A2 had no effect on the proliferation of any of the cell lines tested, indicating a novel growth regulatory role for ATP8A2-Ψ (FIG. 6C). While the knockdown of wild type ATP8A2 had minimal effect on the pseudogene transcript levels, ATP8A2-Ψ specific siRNAs apart from reducing the ATP8A2-Ψ transcript, also reduced the wild type protein levels (FIG. 15B, C). Thus clearly, unlike Oct4 and BRAF pseudogene transcripts having an inverse correlation with the wild type transcript levels, ATP8A2-Ψ and wild-type ATP8A2 transcripts (FIG. 6A,B) and protein (FIG. 15E) are not regulated in this manner. Subsequently, to assess the phenotypic effect of ATP8A2-Ψ overexpression in benign cells, it was cloned and overexpresssed in benign breast epithelial cell line TERT-HMEC. Two independent pooled populations of ATP8A2-Ψ overexpressing TERT-HMEC cells were found to undergo increased proliferation and migration (FIG. 6E) indicating an oncogenic nature of this novel breast specific pseudogene transcript.

Prostate Cancer Pseudogenes

Analysis of tissue-specific pseudogenes restricted to prostate cancers identified numerous pseudogenes, including several derived from parental genes known to be altered or dysregulated in cancer (FIG. 3, right). For example, a prostate cancer pseudogene derived from NDUFA9, which encodes an NADH oxidoreductase component of mitochondrial complex I and is reported to be upregulated in testicular germ cell tumors (Dormeyer et al., 2008 Journal of proteome research 7, 2936-2951) was observed. Pseudogenes derived from EPCAM, whose parental protein-coding gene is an epithelial cell adhesion molecule involved in cancer and stem cells signaling (Munz et al., 2009 Cancer research 69, 5627-5629), PDAP1, that enhances the mitogenic effect of PDGF-A (Fischer and Schubert, 1996 Journal of neurochemistry 66, 2213-2216), RBM17, associated with drug resistance in numerous epithelial cancers (Perry et al., 2005 Cancer research 65, 6593-6600), (Sampath et al., 2003 The American journal of pathology 163, 1781-1790), and CES7, known to be expressed only in the male reproductive tract (Zhang et al., 2009 Acta biochimica et biophysica Sinica 41, 809-815) were also investigated (FIG. 3, right; Table 3). Among the prostate cancer specific pseudogenes, the processed pseudogene CXADR-Ψ, on chromosome 15, was of immediate interest, as the parental CXADR protein demonstrates putative tumor suppressor functions and its loss is implicated in α-catenin silencing (Pong et al., 2003 Cancer research 63, 8680-8686; Stecker et al., 2009 British journal of cancer 101, 1574-1579). This pseudogene was selected for further study in prostate cancer. Independent assays were used to evaluate CXADR-Ψ and parental CXADR gene expression levels using qPCR-based methods. As with ATP8A2-Ψ, upregulation of CXADR-Ψ in ˜25% of prostate cancer tissues, with minimal expression in benign prostate samples and non-prostate tissues was observed (FIG. 5A, top panel). There was no specific relationship between CXADR-Ψ and parental CXADR gene expression, although parental CXADR also had some proclivity for prostate cancer specific expression (FIG. 5A, lower panel). CXADR-Ψ expression was nearly restricted to prostate cancers lacking an ETS gene fusion (FIG. 5A, B), with few ETS-positive samples exhibiting expression of this pseudogene. By contrast, parental CXADR gene expression was found in both ETS-positive and ETSnegative samples (FIG. 5B). CXADR-Ψ and CXADR parental gene expression was assayed in a set of six prostate patients with matched cancer and benign tissues (including four ETS negative and two ETS positive pairs). Again, ETS-negative prostate cancer samples displayed marked upregulation of CXADR-Ψ compared to the ETS-positive patients, with CXADR parental gene expression fairly constant between this set of patients (FIG. 5B, right). As CXADR pseudogene is a processed pseudogene and also less significant mappable difference with respect to its wild type, a significant correlation (R2=0.78) was observed between the expression pattern of RNA-seq and qPCR values (FIG. 14B). As confirmation, the CXADR pseudogene cDNA was cloned and sequences from two index prostate cancer samples, where the resultant sequence mapped 99% mapped to CXADRP2 (pseudogene) and only 84% mapped to CXADR wild type gene.

Lastly, in the course of these analyses, a prostate cancer specific read-through transcript between KLK4, an androgen-induced gene, and KLKP1, an adjacent pseudogene was identified. This read-through results in a chimeric RNA transcript combining the first two exons of KLK4 with the last two exons of KLKP1; and this KLK4-KLKP1 transcript is predicted to retain an open reading frame incorporating 54 amino acids encoded by the KLKP1 pseudogene, indicating that it may encode a chimeric protein (FIG. 16A). This read-through was also recently reported in the LNCaP prostate cancer cell line as a cis sense-antisense chimeric transcript. The KLK4-KLKP1 transcript was highly expressed in 30-50% of prostate cancer tissues, and again this expression was tissue- and cancer-specific, with minimal expression in benign prostate samples and other tissue types (FIG. 16B).

TABLE 1 Sample_ID Flowcell_ lane Sample_Name Tissue_Type Status BL_C_1 42Y2MAAXX.2 BL_C_1 Lymphoma Tumor Tissue BL_C_2 61VFCAAXX.1 BC3 Lymphoma Tumor Cell Line BL_C_3 61VFCAAXX.2 BCP1 Lymphoma Tumor Cell Line BL_C_4 61VFCAAXX.3 BCBL1 Lymphoma Tumor Cell Line BL_C_5 6286PAAXX.8 RPMI_6666 Lymphoma Tumor Cell Line BL_N_C_1 302LVAAXX.5 HCC1428_BL Lymphoblastoid Benign Cell Line BL_N_C_2 302LVAAXX.6 HCC1937_BL Lymphoblastoid Benign Cell Line BL_N_C_3 302LVAAXX.7 HCC1187_BL Lymphoblastoid Benign Cell Line BL_N_C_4 42TCLAAXX.1, HCC38_BL Lymphoblastoid Benign Cell Line 42Y39AAXX.2 BL_N_C_5 42TCLAAXX.3, HCC1599_BL Lymphoblastoid Benign Cell Line 42Y39AAXX.5 BL_N_C_6 42TCLAAXX.4, HCC2157_BL Lymphoblastoid Benign Cell Line 42Y39AAXX.6 BL_N_C_7 42TCLAAXX.5, HCC2218_BL Lymphoblastoid Benign Cell Line 42Y39AAXX.7 BL_N_C_8 42Y39AAXX.3, HCC1143_BL Lymphoblastoid Benign Cell Line 42Y39AAXX.4 BL_T_1 42Y2MAAXX.1 BL_T_1 Chronic Tumor Tissue Lymphocytic Leukemia BL_T_2 42Y2MAAXX.3 BL_T_2 Chronic Tumor Tissue Lymphocytic Leukemia BL_T_3 42Y2MAAXX.4 BL_T_3 Chronic Tumor Tissue Lymphocytic Leukemia BL_T_4 42Y2MAAXX.5 BL_T_4 Chronic Tumor Tissue Lymphocytic Leukemia BL_T_5 42Y2MAAXX.6 BL_T_5 Chronic Tumor Tissue Lymphocytic Leukemia BL_T_6 42Y2MAAXX.7 BL_T_6 Chronic Tumor Tissue Lymphocytic Leukemia Bld_T_1 42RMPAAXX.5 Bld_T_1 Bladder Tumor Tissue Bld_T_2 42RMPAAXX.6 Bld_T_2 Bladder Tumor Tissue Bld_T_3 42TCBAAXX.1 Bld_T_3 Bladder Tumor Tissue Bld_T_4 42TCBAAXX.2 Bld_T_4 Bladder Tumor Tissue Bld_T_5 42TCBAAXX.3 Bld_T_5 Bladder Tumor Tissue Bld_T_6 42TCBAAXX.4 Bld_T_6 Bladder Tumor Tissue Bld_T_7 42TCBAAXX.5 Bld_T_7 Bladder Tumor Tissue Bld_T_8 42TCBAAXX.6 Bld_T_8 Bladder Tumor Tissue Bld_T_9 42TCBAAXX.7 Bld_T_9 Bladder Tumor Tissue Bld_T_10 42TCBAAXX.8 Bld_T_10 Bladder Tumor Tissue Bld_T_11 42TG0AAXX.2 Bld_T_11 Bladder Tumor Tissue Bld_T_12 42TG0AAXX.3 Bld_T_12 Bladder Tumor Tissue Bld_T_13 42TG0AAXX.4 Bld_T_13 Bladder Tumor Tissue Bld_T_14 42TG0AAXX.5 Bld_T_14 Bladder Tumor Tissue Bld_T_15 42TG0AAXX.6 Bld_T_15 Bladder Tumor Tissue Bld_T_16 42TG0AAXX.7 Bld_T_16 Bladder Tumor Tissue Bld_T_17 42TG0AAXX.8 Bld_T_17 Bladder Tumor Tissue Br_C_1 42PMUAAXX.5 HCC38 Breast Tumor Cell Line Br_C_2 42D3NAAXX.4, HCC1008 Breast Tumor Cell Line 42Y39AAXX.8 Br_C_3 3035BAAXX.3 HCC1143 Breast Tumor Cell Line Br_C_4 314NNAAXX.3, HCC1395 Breast Tumor Cell Line 314WAAAXX.3 Br_C_5 314WAAAXX.5, HCC1599 Breast Tumor Cell Line 42Y39AAXX.1 Br_C_6 30WB6AAXX.7 HCC1937 Breast Tumor Cell Line Br_C_7 30LEJAAXX.7 MCF7 Breast Tumor Cell Line Br_C_8 315CUAAXX.3 ZR-75-1 Breast Tumor Cell Line Br_C_9 314WAAAXX.4 HCC1954 Breast Tumor Cell Line Br_C_10 42PMUAAXX.3 HCC2157 Breast Tumor Cell Line Br_C_11 6137LAAXX.2 MDA-MB-231 Breast Tumor Cell Line Br_C_12 30Y6GAAXX.1, MDA-MB-361 Breast Tumor Cell Line 314NNAAXX.5 Br_C_13 30Y6GAAXX.3 MDA-MB-435S Breast Tumor Cell Line Br_C_14 30LUMAAXX.3, T-47D Breast Tumor Cell Line 314WGAAXX.1 Br_C_15 302LVAAXX.2 HCC1187 Breast Tumor Cell Line Br_C_16 3035BAAXX.2 ZR-75-30 Breast Tumor Cell Line Br_C_17 3035BAAXX.5 HCC1428 Breast Tumor Cell Line Br_C_18 3035BAAXX.6 HCC1419 Breast Tumor Cell Line Br_C_19 30650AAXX.5 UACC-812_T Breast Tumor Cell Line Br_C_20 30650AAXX.6 UACC-893_T Breast Tumor Cell Line Br_C_21 30650AAXX.7 MDA-MB-330 Breast Tumor Cell Line Br_C_22 30WB6AAXX.5, MDA-MB-134-VI Breast Tumor Cell Line 315CUAAXX.4 Br_C_23 30WB6AAXX.6 HCC70 Breast Tumor Cell Line Br_C_24 30Y6GAAXX.2 CAMA-1 Breast Tumor Cell Line Br_C_25 314NNAAXX.2 MDA-MB-175-VII Breast Tumor Cell Line Br_C_26 314RPAAXX.5 HCC2218 Breast Tumor Cell Line Br_C_27 314RPAAXX.7 BT-483 Breast Tumor Cell Line Br_C_28 314WAAAXX.1 BT-20 Breast Tumor Cell Line Br_C_29 314WAAAXX.2 BT-549 Breast Tumor Cell Line Br_C_30 314WAAAXX.7 Hs-578T Breast Tumor Cell Line Br_C_31 314WGAAXX.5 HCC1569 Breast Tumor Cell Line Br_C_32 314WGAAXX.7 MDA-MB-157 Breast Tumor Cell Line Br_C_33 315CUAAXX.1 MDA-MB-453 Breast Tumor Cell Line Br_C_34 315CUAAXX.2 MDA-MB-468 Breast Tumor Cell Line Br_C_35 429T4AAXX.1 HCC202 Breast Tumor Cell Line Br_C_36 42HAMAAXX.3 DU4475 Breast Tumor Cell Line Br_C_37 42HAMAAXX.5 HCC1500 Breast Tumor Cell Line Br_C_38 42PFAAAXX.7 SUM_149PT Breast Tumor Cell Line Br_C_39 42PFAAAXX.8 SUM_190PT Breast Tumor Cell Line Br_C_40 42PMUAAXX.1 MDA-MB-436 Breast Tumor Cell Line Br_C_41 42PMUAAXX.2 MDA-MB-415 Breast Tumor Cell Line Br_N_C_1 30Y6GAAXX.6 MCF12A Breast Benign Cell Line Br_N_C_2 30Y6GAAXX.7 MCF10A Breast Benign Cell Line Br_N_C_3 314NNAAXX.4 MCF10F Breast Benign Cell Line Br_N_C_4 314RPAAXX.6 HMEC1 Breast Benign Cell Line Br_N_C_5 314WAAAXX.6 HBL-100 Breast Benign Cell Line Br_N_C_6 42B3YAAXX.S H16N2 Breast Benign Cell Line Br_N_C_7 42B3YAAXX.6 hTERT-HME1 Breast Benign Cell Line Br_N_C_8 42B3YAAXX.7 HMEC2 Breast Benign Cell Line Br_N_T_1 30Y6GAAXX.4 Br_N_T_1 Breast Benign Tissue Br_N_T_2 30Y6GAAXX.5 Br_N_T_2 Breast Benign Tissue Br_N_T_3 42PMUAAXX.4 Br_N_T_3 Breast Benign Tissue Br_T_1 30U00AAXX.1 Br_T_1 Breast Tumor Tissue Br_T_2 30GC3AAXX.1 Br_T_2 Breast Tumor Tissue Br_T_3 30GC3AAXX.2 Br_T_3 Breast Tumor Tissue Br_T_4 30U00AAXX.2 Br_T_4 Breast Metastatic Tissue Br_T_5 30U00AAXX.3 Br_T_5 Breast Metastatic Tissue Br_T_6 314N5AAXX.1 Br_T_6 Breast Tumor Tissue Br_T_7 314N5AAXX.2 Br_T_7 Breast Tumor Tissue Br_T_8 314N5AAXX.3 Br_T_8 Breast Tumor Tissue Br_T_9 314N5AAXX.4 Br_T_9 Breast Tumor Tissue Br_T_10 315CUAAXX.5 Br_T_10 Breast Tumor Tissue Br_T_11 315CUAAXX.6 Br_T_11 Breast Tumor Tissue Br_T_12 315CUAAXX.7 Br_T_12 Breast Tumor Tissue Cer_C_1 30Y5NAAXX.2, Caski Cervical Tumor Cell Line 42Y6NAAXX.3 Cer_C_2 42Y6NAAXX.1 C-33_A Cervical Tumor Cell Line Cer_C_3 42Y6NAAXX.2 C-4_II Cervical Tumor Cell Line Cer_C_4 42Y6NAAXX.4 HeLa Cervical Tumor Cell Line Cer_C_5 42Y6NAAXX.5 MS751 Cervical Tumor Cell Line Cer_C_6 42Y6NAAXX.6 HT-3 Cervical Tumor Cell Line Cer_C_7 42Y6NAAXX.7 ME-180 Cervical Tumor Cell Line Cer_C_8 42Y6NAAXX.8 SiHa Cervical Tumor Cell Line CL_C_1 61VFCAAXX.6 HCT-15 Colon Tumor Cell Line CL_C_2 6286PAAXX.3 SW620 Colon Tumor Cell Line CL_C_3 6286PAAXX.4 HT-29 Colon Tumor Cell Line CL_C_4 6286PAAXX.5 HCT_116 Colon Tumor Cell Line CL_C_5 6286PAAXX.6 COLO_205 Colon Tumor Cell Line CL_C_6 6286PAAXX.7 SW837 Colon Tumor Cell Line Gst_C_1 42RMPAAXX.7 YCC-16 Gastric Tumor Cell Line Gst_C_2 42RMPAAXX.8 YCC-3 Gastric Tumor Cell Line Gst_C_3 42Y6WAAXX.2, AZ-521 Gastric Tumor Cell Line 42YMTAAXX.2 Gst_C_4 42YMMAAXX.1 IM95 Gastric Tumor Cell Line Gst_C_5 42YMMAAXX.2, MKN-28 Gastric Tumor Cell Line 42YMMAAXX.8 Gst_C_6 42YMMAAXX.3 AGS Gastric Tumor Cell Line Gst_C_7 42YMMAAXX.4 NCI-N87 Gastric Tumor Cell Line Gst_C_8 42YMTAAXX.1 SNU-16 Gastric Tumor Cell Line Gst_N_T_1 42RYFAAXX.6 Gst_N_T_1 Gastric Benign Tissue Gst_N_T_2 42RYFAAXX.7 Gst_N_T_2 Gastric Benign Tissue Gst_N_T_3 42RYFAAXX.8 Gst_N_T_3 Gastric Benign Tissue Gst_N_T_4 42YMTAAXX.7 Gst_N_T_4 Gastric Benign Tissue Gst_T_1 42RYFAAXX.1 Gst_T_1 Gastric Tumor Tissue Gst_T_2 42RYFAAXX.2 Gst_T_2 Gastric Tumor Tissue Gst_T_3 42RYFAAXX.3 Gst_T_3 Gastric Tumor Tissue Gst_T_4 42RYFAAXX.4 Gst_T_4 Gastric Tumor Tissue Gst_T_5 42RYFAAXX.5 Gst_T_5 Gastric Tumor Tissue Gst_T_6 42Y6WAAXX.3, Gst_T_6 Gastric Tumor Tissue 42YMTAAXX.4 Gst_T_7 42Y6WAAXX.4, Gst_T_7 Gastric Benign Tissue 42YMTAAXX.8 Gst_T_8 42YMMAAXX.5 Gst_T_8 Gastric Tumor Tissue Gst_T_9 42YMMAAXX.6 Gst_T_9 Gastric Tumor Tissue Gst_T_10 42YMMAAXX.7 Gst_T_10 Gastric Tumor Tissue Gst_T_11 42YMTAAXX.3 Gst_T_11 Gastric Tumor Tissue Gst_T_12 42YMTAAXX.5 Gst_T_12 Gastric Tumor Tissue Gst_T_13 42YMTAAXX.6 Gst_T_13 Gastric Tumor Tissue Ky_T_1 42RMPAAXX.1 Ky_T_1 Renal Tumor Tissue Ky_T_2 42RMPAAXX.2 Ky_T_2 Renal Tumor Tissue Ky_T_3 42RMPAAXX.3 Ky_T_3 Renal Tumor Tissue Ky_T_4 42RMPAAXX.4 Ky_T_4 Renal Tumor Tissue Ky_T_5 42TBWAAXX.1 Ky_T_5 Renal Tumor Tissue Ky_T_6 42TBWAAXX.2 Ky_T_6 Renal Tumor Tissue Ky_T_7 42TBWAAXX.3 Ky_T_7 Renal Tumor Tissue Ky_T_8 42TBWAAXX.4 Ky_T_8 Renal Tumor Tissue Ky_T_9 42TBWAAXX.5 Ky_T_9 Renal Tumor Tissue Ky_T_10 42TBWAAXX.6, Ky_T_10 Renal Tumor Tissue 42Y6WAAXX.1 Ky_T_11 42TBWAAXX.7 Ky_T_11 Renal Tumor Tissue Ky_T_12 42TBWAAXX.8 Ky_T_12 Renal Tumor Tissue Mel_C_1 42YRVAAXX.2 SK-MEL-173 Melanoma Tumor Cell Line Mel_C_2 42B20AAXX.2 SK-MEL-94 Melanoma Tumor Cell Line Mel_C_3 42HAMAAXX.1 MM96L Melanoma Tumor Cell Line Mel_C_4 42B20AAXX.1 D14 Melanoma Tumor Cell Line Mel_C_5 42YRVAAXX.3 MelCelline_Z Melanoma Tumor Cell Line Mel_C_6 42HAMAAXX.2 SK-MEL-5 Melanoma Tumor Cell Line Mel_C_7 42YRVAAXX.1 SK-MEL-28 Melanoma Tumor Cell Line Mel_N_T_1 3035BAAXX.1 MelN_T_1 Melanocyte Benign Tissue Mel_T_1 42PF0AAXX.6 Mel_T_1 Melanoma Tumor Tissue Mel_T_2 42PF0AAXX.7 Mel_T_2 Melanoma Tumor Tissue MPN_T_1 6137KAAXX.8 MPN_T_1 MPN Tumor Tissue MPN_T_2 62837AAXX.1 MPN_T_2 MPN Tumor Tissue MPN_T_3 62837AAXX.2 MPN_T_3 MPN Tumor Tissue MPN_T_4 62837AAXX.3 MPN_T_4 MPN Tumor Tissue MPN_T_5 62837AAXX.4 MPN_T_5 MPN Tumor Tissue MPN_T_6 62837AAXX.7 MPN_T_6 MPN Tumor Tissue MPN_T_7 62837AAXX.8 MPN_T_7 MPN Tumor Tissue MPN_T_8 6286PAAXX.1 MPN_T_8 MPN Tumor Tissue MPN_T_9 6286PAAXX.2 MPN_T_9 MPN Tumor Tissue OC_C_1 6137KAAXX.6 CGHNK6 Oral Tumor Cell Line OC_C_2 6137KAAXX.7 TW2.6 Oral Tumor Cell Line PAN_C_1 314N5AAXX.6 BxPC-3 Pancreas Tumor Cell Line PAN_C_2 314WGAAXX.4 MIA-PaCa-2 Pancreas Tumor Cell Line PAN_C_3 30Y5NAAXX.1, PANC-1 Pancreas Tumor Cell Line 315C1AAXX.1 PAN_C_4 30LUMAAXX.2, Panc-10.05 Pancreas Tumor Cell Line 42AV4AAXX.4 PAN_C_5 314N5AAXX.5 HPAF-II Pancreas Tumor Cell Line PAN_C_6 42HAMAAXX.7 AsPC-1 Pancreas Tumor Cell Line PAN_C_7 314N5AAXX.7 Capan-2 Pancreas Tumor Cell Line PAN_C_8 30650AAXX.1 Panc-05.04 Pancreas Tumor Cell Line PAN_C_9 30WG6AAXX.5 Hs-766T Pancreas Tumor Cell Line PAN_C_10 314WGAAXX.2 Capan-1 Pancreas Tumor Cell Line PAN_C_11 314WGAAXX.3 HPAC Pancreas Tumor Cell Line PAN_C_13 315C1AAXX.3 CFPAC-1 Pancreas Tumor Cell Line PAN_C_14 315C1AAXX.4 SU.86.86 Pancreas Tumor Cell Line PAN_C_16 42AV4AAXX.1 Hs-700T Pancreas Tumor Cell Line PAN_C_17 42AV4AAXX.2 PL45 Pancreas Tumor Cell Line PAN_C_18 42AV4AAXX.3 L3.3 Pancreas Tumor Cell Line PAN_C_19 42AV4AAXX.5 Panc-08.13 Pancreas Tumor Cell Line PAN_C_20 42AV4AAXX.6 Panc-02.03 Pancreas Tumor Cell Line PAN_C_21 42AV4AAXX.7 Panc-02.13 Pancreas Tumor Cell Line PAN_C_22 42HAMAAXX.6 Panc-03.27 Pancreas Tumor Cell Line PAN_C_23 42CJJAAXX.1 Panc-04.03 Pancreas Tumor Cell Line PAN_N_C_1 30WG6AAXX.6 HPNE Pancreas Benign Cell Line PAN_N_C_2 30WG6AAXX.7 HPDE Pancreas Benign Cell Line PAN_N_T_1 30WG6AAXX.4 PAN_N_T_1 Pancreas Benign Tissue PAN_T_1 42CJJAAXX.2 PAN_T_1 Pancreas Tumor Tissue PAN_T_2 42CJJAAXX.3 PAN_T_2 Pancreas Tumor Tissue PAN_T_3 42CJJAAXX.4 PAN_T_3 Pancreas Tumor Tissue PAN_T_4 42PMUAAXX.8 PAN_T_4 Pancreas Tumor Tissue PR_C_1 30TUEAAXX.3 VCaP Prostate Tumor Cell Line PR_C_2 314NNAAXX.6 22Rv1 Prostate Tumor Cell Line PR_C_3 3064YAAXX.1, PC3 Prostate Tumor Cell Line 30LF7AAXX.1 PR_C_4 429T4AAXX.2 C4-2B Prostate Metastatic Cell Line PR_C_5 429T4AAXX.3 LAPC-4 Prostate Tumor Cell Line PR_C_6 429T4AAXX.4 NCI-H660 Prostate Metastatic Cell Line PR_C_7 429T4AAXX.5 CA-HPV.10 Prostate Tumor Cell Line PR_C_8 429T4AAXX.6 MDA-PCa-2B Prostate Metastatic Cell Line PR_C_9 429T4AAXX.7 CWR22 Prostate Tumor Cell Line PR_C_10 42B08AAXX.2 PWR-1E Prostate Benign Cell Line PR_C_12 42B08AAXX.4 WPE1-NB26 Prostate Metastatic Cell Line PR_C_13 42PFAAAXX.5, LNCaP Prostate Metastatic Cell Line 42PFAAAXX.6, 42PMUAAXX.6, 42PMUAAXX.7 PR_C_17 42TA8AAXX.1, DU-145 Prostate Tumor Cell Line 42TA8AAXX.2, 42TA8AAXX.3, 42TA8AAXX.4, 42TA8AAXX.5, 42TA8AAXX.6, 42TA8AAXX.7 PR_N_C_1 30351AAXX.7, PrEC Prostate Benign Cell Line 314T1AAXX.1 PR_N_C_2 30LEJAAXX.2 RWPE Prostate Benign Cell Line PR_N_C_3 314T1AAXX.2 PrSMC Prostate Benign Cell Line PR_N_T_1 30LF7AAXX.2 PR_N_T_1 Prostate Benign Tissue PR_N_T_2 30LF7AAXX.3 PR_N_T_2 Prostate Benign Tissue PR_N_T_3 301YWAAXX.1, PR_N_T_3 Prostate Benign Tissue 42P6UAAXX.4 PR_N_T_4 3064YAAXX.2, PR_N_T_4 Prostate Benign Tissue 42P6UAAXX.1 PR_N_T_5 3064YAAXX.3, PR_N_T_5 Prostate Benign Tissue 42P6UAAXX.2 PR_N_T_6 3064YAAXX.7, PR_N_T_6 Prostate Benign Tissue 42P6UAAXX.3 PR_N_T_9 30TUEAAXX.2 PR_N_T_9 Prostate Benign Tissue PR_N_T_10 30TUEAAXX.7 PR_N_T_10 Prostate Benign Tissue PR_N_T_11 30TUEAAXX.1 PR_N_T_11 Prostate Benign Tissue PR_N_T_12 30TUEAAXX.8 PR_N_T_12 Prostate Benign Tissue PR_N_T_17 30WU2AAXX.5, PR_N_T_17 Prostate Benign Tissue 42B48AAXX.4 PR_N_T_18 30WU2AAXX.6, PR_N_T_18 Prostate Benign Tissue 42B48AAXX.8, 42PFAAAXX.2 PR_N_T_19 42B20AAXX.5, PR_N_T_19 Prostate Benign Tissue 42NY4AAXX.6 PR_N_T_20 42B48AAXX.1, PR_N_T_20 Prostate Benign Tissue 42NY4AAXX.3 PR_N_T_21 42D3NAAXX.5 PR_N_T_21 Prostate Benign Tissue PR_T_1 30TYGAAXX.1 PR_T_1 Prostate Metastatic Tissue PR_T_2 30TYGAAXX.3 PR_T_2 Prostate Metastatic Tissue PR_T_3 42B20AAXX.6 PR_T_3 Prostate Metastatic Tissue PR_T_5 30U00AAXX.7 PR_T_5 Prostate Metastatic Tissue PR_T_7 30TYGAAXX.5 PR_T_7 Prostate Metastatic Tissue PR_T_10 301YWAAXX.2, PR_T_10 Prostate Tumor Tissue 42P6UAAXX.5 PR_T_11 301YWAAXX.3 PR_T_11 Prostate Tumor Tissue PR_T_12 3064YAAXX.4, PR_T_12 Prostate Tumor Tissue 30JD2AAXX.6 PR_T_13 3064YAAXX.5 PR_T_13 Prostate Metastatic Tissue PR_T_14 3064YAAXX.6 PR_T_14 Prostate Metastatic Tissue PR_T_15 30Y5NAAXX.3, PR_T_15 Prostate Tumor Tissue 42B48AAXX.7 PR_T_16 30Y5NAAXX.4, PR_T_16 Prostate Tumor Tissue 42CJFAAXX.2, 42NY4AAXX.5 PR_T_17 30GC3AAXX.3, PR_T_17 Prostate Tumor Tissue 30Y5NAAXX.6 PR_T_18 30Y5NAAXX.7 PR_T_18 Prostate Tumor Tissue PR_T_19 30TUEAAXX.5 PR_T_19 Prostate Tumor Tissue PR_T_20 30TUEAAXX.6 PR_T_20 Prostate Tumor Tissue PR_T_21 30GC3AAXX.5 PR_T_21 Prostate Tumor Tissue PR_T_22 30GC3AAXX.6, PR_T_22 Prostate Tumor Tissue 30JD2AAXX.5 PR_T_23 30JD2AAXX.3 PR_T_23 Prostate Tumor Tissue PR_T_24 30JD2AAXX.7 PR_T_24 Prostate Tumor Tissue PR_T_25 30JD2AAXX.8 PR_T_25 Prostate Tumor Tissue PR_T_27 30U00AAXX.4 PR_T_27 Prostate Tumor Tissue PR_T_28 30U00AAXX.5, PR_T_28 Prostate Metastatic Tissue 30U00AAXX.6, 42B08AAXX.6 PR_T_29 30WU2AAXX.1, PR_T_29 Prostate Tumor Tissue 42B08AAXX.1, 42CJJAAXX.5 PR_T_30 42CJJAAXX.7, PR_T_30 Prostate Benign Tissue 42NY4AAXX.2 PR_T_31 42B48AAXX.2, PR_T_31 Prostate Tumor Tissue 42PFAAAXX.1 PR_T_32 30WU2AAXX.4, PR_T_32 Prostate Tumor Tissue 42B48AAXX.3 PR_T_33 30WU2AAXX.7, PR_T_33 Prostate Benign Tissue 42CJFAAXX.5 PR_T_34 30WU2AAXX.8, PR_T_34 Prostate Tumor Tissue 42CJFAAXX.4, 42PFAAAXX.3 PR_T_36 42B08AAXX.5 PR_T_36 Prostate Tumor Tissue PR_T_37 42B08AAXX.7 PR_T_37 Prostate Tumor Tissue PR_T_38 42B08AAXX.8 PR_T_38 Prostate Tumor Tissue PR_T_39 42B3YAAXX.4 PR_T_39 Prostate Tumor Tissue PR_T_40 42B48AAXX.5 PR_T_40 Prostate Tumor Tissue PR_T_41 42B48AAXX.6, PR_T_41 Prostate Tumor Tissue 42NY4AAXX.4 PR_T_42 42CJFAAXX.1 PR_T_42 Prostate Tumor Tissue PR_T_44 42CJFAAXX.6 PR_T_44 Prostate Metastatic Tissue PR_T_45 42CJFAAXX.7, PR_T_45 Prostate Tumor Tissue 42P6UAAXX.8, 42PFAAAXX.4 PR_T_47 42CJJAAXX.6, PR_T_47 Prostate Tumor Tissue 42PF0AAXX.3 PR_T_48 42CJJAAXX.8 PR_T_48 Prostate Tumor Tissue PR_T_49 42D3NAAXX.1 PR_T_49 Prostate Tumor Tissue PR_T_50 42D3NAAXX.2 PR_T_50 Prostate Tumor Tissue PR_T_51 42D3NAAXX.3 PR_T_51 Prostate Tumor Tissue PR_T_52 42D3NAAXX.6, PR_T_52 Prostate Tumor Tissue 42P6UAAXX.6 PR_T_53 42D3NAAXX.7, PR_T_53 Prostate Tumor Tissue 42P6UAAXX.7 PR_T_54 42TB9AAXX.1 PR_T_54 Prostate Tumor Tissue PR_T_55 42TB9AAXX.2 PR_T_55 Prostate Tumor Tissue PR_T_56 42TB9AAXX.3 PR_T_56 Prostate Tumor Tissue PR_T_57 42TB9AAXX.4, PR_T_57 Prostate Tumor Tissue 42Y6WAAXX.6 PR_T_58 42TB9AAXX.6 PR_T_58 Prostate Tumor Tissue PR_T_59 42TB9AAXX.7 PR_T_59 Prostate Tumor Tissue PR_T_60 42Y2MAAXX.8 PR_T_60 Prostate Tumor Tissue PR_T_61 43336AAXX.1 PR_T_61 Prostate Tumor Tissue PR_T_62 43336AAXX.2 PR_T_62 Prostate Tumor Tissue PR_T_63 43336AAXX.3 PR_T_63 Prostate Tumor Tissue PR_T_64 6137KAAXX.3, PR_T_64 Prostate Metastatic Tissue 6137KAAXX.4, 6137LAAXX.6 PR_T_65 6137LAAXX.7 PR_T_65 Prostate Tumor Tissue PR_T_66 6137LAAXX.8 PR_T_66 Prostate Tumor Tissue SG_T_1 43336AAXX.4 SG_T_1 Salivary Tumor Tissue Gland SG_T_2 43336AAXX.5 SG_T_2 Salivary Tumor Tissue Gland SG_T_3 43336AAXX.6 SG_T_3 Salivary Tumor Tissue Gland SG_T_4 43336AAXX.7 SG_T_4 Salivary Tumor Tissue Gland

TABLE 2 Flowcell_lane Total_Count PF_Count hs_ref_chr1 hs_ref_chr2 hs_ref_chr3 hs_ref_chr4 hs_ref_chr5 314N5AAXX_6 10473424 8629317 891576 303708 315512 138671 224453 314WGAAXX_4 10220916 8510626 815415 383727 297329 123995 297034 30Y5NAAXX_1 21397810 10789719 1044813 501271 371407 168358 358977 315C1AAXX_1 20993016 8320198 777760 372380 285462 122081 274471 30LUMAAXX_2 11963090 7629386 694396 431203 326417 145063 264302 42AV4AAXX_4 23950519 18405648 1760521 831675 624394 339165 596817 314N5AAXX_5 10917232 9001619 771148 477219 392899 172329 307359 30TYGAAXX_1 10401208 7749518 202168 108883 89364 51464 79768 42PMUAAXX_5 10075786 8835013 814959 498501 320439 149215 281021 42D3NAAXX_4 11728387 9472843 889762 367340 322203 122027 227293 42Y39AAXX_8 22686263 16753241 1615986 684121 587253 243140 444007 42YRVAAXX_2 24910111 9952386 972856 462262 351827 204328 349844 42B20AAXX_2 15027956 13454580 1402697 485225 387638 173940 471147 30TYGAAXX_3 9461708 6778936 279229 149660 111711 85437 94044 42B20AAXX_6 15024331 13826315 1457854 486905 556446 224286 347700 42HAMAAXX_1 12153995 10924998 1210269 443524 368971 188525 449786 42B20AAXX_1 20012752 16653225 1742015 777175 720316 290880 512558 42YRVAAXX_3 15502449 13197913 1184945 558602 516507 209748 400480 42HAMAAXX_2 18573826 15911042 1242358 615536 555506 239122 489876 42YRVAAXX_1 24214865 8771902 873593 539427 323245 146812 274181 30TUEAAXX_3 8514234 6557403 428806 251831 260722 136415 180308 3035BAAXX_3 14593087 10308363 875982 386468 346520 140189 358437 314NNAAXX_3 8208384 6641235 601367 308758 229249 87188 207361 314WAAAXX_3 12230961 8474905 778636 392304 295037 121843 262822 314WAAAXX_5 10190342 6844572 761087 314352 302378 119767 214689 42Y39AAXX_1 23513773 16997748 1996837 845432 808437 331682 581896 30WB6AAXX_7 11819695 9295846 769796 316001 386746 142076 322589 30351AAXX_7 14162607 8883459 960562 470335 361236 216694 299455 314T1AAXX_1 12509198 7748627 818152 364685 284298 161372 233107 30U00AAXX_7 17567068 9138228 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314WGAAXX_1 12754073 9789340 912346 307728 407574 152807 338065 42HAMAAXX_7 10819606 9632982 820121 433856 251257 147426 282843 314N5AAXX_7 10289131 8391763 857681 370661 344924 214015 305391 301YWAAXX_1 16784282 14755517 1254041 731559 550897 280867 424454 42P6UAAXX_4 19556063 16107801 1371541 794583 610961 309131 466080 301YWAAXX_2 15547938 14017921 1259951 711252 531236 291695 434508 42P6UAAXX_5 16096802 14031093 1254148 704316 531914 293325 434091 301YWAAXX_3 15995869 14290078 1284093 685587 501233 283207 384288 302LVAAXX_2 15811517 11110453 1245685 377497 312585 186718 301958 302LVAAXX_5 15661470 11158691 1055556 474996 391414 203743 413507 302LVAAXX_6 15468054 10988635 1185976 476401 436448 250860 436990 302LVAAXX_7 16094827 11172977 1085306 494116 415332 222285 410366 3035BAAXX_1 14440359 10322757 880960 438978 353826 183989 308704 3035BAAXX_2 17310015 11763778 1143851 457215 381332 227189 328779 3035BAAXX_5 18670237 11765186 1152166 558818 371277 159952 278184 3035BAAXX_6 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204644 70034 240010 103007 855 381926 43066 314WGAAXX_5 370359 103175 225164 197402 1134 410446 47381 314WGAAXX_7 169076 62192 118793 278103 871 483810 92377 315C1AAXX_3 216424 69241 167846 148894 3090 214493 15292 315C1AAXX_4 239677 66296 176426 109906 1000 338711 28474 315CUAAXX_1 170575 48443 327916 213699 534 163300 37807 315CUAAXX_2 214352 110465 231279 291690 4468 512214 30544 315CUAAXX_5 247759 101772 352628 232916 3556 673610 111769 315CUAAXX_6 202014 74793 185387 135719 1264 551234 98533 315CUAAXX_7 172658 80746 199194 189783 962 777467 77675 429T4AAXX_1 249551 119718 281242 419753 4830 1601258 126735 429T4AAXX_2 267925 72106 351351 252611 1330 730772 199496 429T4AAXX_3 388148 137093 303818 321912 19998 1169947 193719 429T4AAXX_4 329878 105710 216856 282643 3086 742024 116066 429T4AAXX_5 404052 90265 183739 267473 6151 605693 50507 429T4AAXX_6 262807 114283 315127 242597 10509 485941 127036 429T4AAXX_7 264053 94533 359557 239140 11195 623870 194650 42AV4AAXX_1 420874 119406 236308 324944 13005 2120354 54167 42AV4AAXX_2 400046 78473 205630 301395 2445 2048491 47456 42AV4AAXX_3 463306 97799 324461 325154 1737 2062037 34842 42AV4AAXX_5 377952 115991 338960 270580 4824 1058598 61186 42AV4AAXX_6 482705 131023 434882 276641 1707 1227106 56910 42AV4AAXX_7 498381 112400 291280 410671 3349 869650 83496 42B08AAXX_2 271150 63237 220901 148004 2634 215196 26720 42B08AAXX_4 300359 66867 135530 185060 437 392084 54559 42B08AAXX_5 210323 98698 214852 224405 10427 917319 251404 42B08AAXX_7 265481 117534 255708 290859 9411 1051916 311425 42B08AAXX_8 205319 92302 223358 202092 9962 1180031 340986 42B20AAXX_5 362137 148783 357877 394729 12389 1424912 68003 42NY4AAXX_6 341976 141231 337090 375487 12052 1378888 64209 42B3YAAXX_4 138246 70875 136382 138391 12304 616691 49451 42B3YAAXX_5 170648 70467 168072 135388 974 566518 42326 42B3YAAXX_6 132475 44905 136459 160395 389 667026 26299 42B3YAAXX_7 113408 43048 107718 141494 2593 1283890 22330 42B48AAXX_1 256567 124172 269332 265243 10027 983648 157164 42NY4AAXX_3 251137 121415 265584 257036 9430 928636 161751 42B48AAXX_5 289925 151138 324297 301082 16442 839180 118722 42B48AAXX_6 268154 131026 276605 289938 13242 350851 117843 42NY4AAXX_4 266872 131493 274396 290415 12943 342377 123414 42HAMAAXX_3 209625 75012 179009 178200 1219 1534882 129974 42HAMAAXX_5 298877 111530 239274 229981 3278 2034501 56439 42HAMAAXX_6 269900 74133 186667 225872 2058 893981 50924 42CJFAAXX_1 199515 94642 214310 212679 8137 619494 95565 42CJFAAXX_6 213143 65160 209320 243647 2492 888964 192749 42CJFAAXX_7 167097 81067 176950 172649 8986 1424677 227067 42P6UAAXX_8 17215 8261 18561 17295 838 127745 27005 42PFAAAXX_4 234903 114839 247425 241570 13148 2053928 301739 42CJJAAXX_1 609310 96684 339568 295849 2164 989128 66148 42CJJAAXX_2 737464 63851 124388 275901 7126 3216582 130981 42CJJAAXX_3 620338 114045 191753 270642 1229 2838056 84081 42CJJAAXX_4 354431 85810 232698 336192 2110 3523049 100011 42CJJAAXX_6 297926 49000 122836 111915 5030 158056 119060 42PF0AAXX_3 474196 75648 186927 171612 7865 243691 175886 42CJJAAXX_8 276176 156128 314108 276910 12822 1482316 145473 42D3NAAXX_1 149531 76670 149834 155396 6781 909739 6467 42D3NAAXX_2 174357 81452 187633 155803 7382 986739 16225 42D3NAAXX_3 203877 99595 228529 197506 7263 1180391 24387 42D3NAAXX_5 216461 104278 243974 224609 10383 575251 183145 42D3NAAXX_6 216570 94026 248425 210652 6989 968227 101922 42P6UAAXX_6 262878 115240 301391 255754 8489 1184336 125429 42D3NAAXX_7 209014 111163 245063 178246 9808 748009 134024 42P6UAAXX_7 275545 147193 323736 233642 12781 997498 178517 42PF0AAXX_6 166272 77755 189860 252159 1035 3676417 226269 42PF0AAXX_7 172728 77054 166483 207201 697 747677 138139 42PFAAAXX_5 284380 85891 227994 270434 1701 2327751 49276 42PFAAAXX_6 208760 92853 146553 220040 15640 3028379 15541 42PMUAAXX_6 219362 83814 183818 207903 1308 1459593 42587 42PMUAAXX_7 197489 65724 166683 189731 6249 1195127 34780 42PFAAAXX_7 358890 109693 196656 272956 2409 2148064 93843 42PFAAAXX_8 163790 97732 299455 202865 2498 1402728 49005 42PMUAAXX_1 249100 88440 184288 420975 1051 485068 75760 42PMUAAXX_2 215351 49403 185381 197459 5227 2014100 33040 42PMUAAXX_4 153323 80214 178254 154882 996 789484 30244 42PMUAAXX_8 333209 72183 47727 152540 649 1083625 10980 42RMPAAXX_1 352483 146277 315190 373134 1534 2434765 85843 42RMPAAXX_2 326773 158346 290994 408029 26840 1939964 58283 42RMPAAXX_3 283991 129844 372065 360638 7922 2100050 80609 42RMPAAXX_4 232371 84290 280856 229378 13327 6164636 110174 42RMPAAXX_5 229712 79564 173748 249338 2193 1843288 13102 42RMPAAXX_6 198544 65203 101217 195516 4462 1440663 57432 42RMPAAXX_7 220849 55137 123864 283485 10462 532142 35666 42RMPAAXX_8 405746 80304 269425 281905 1106 482264 82124 42RYFAAXX_1 126325 58501 139344 108355 2024 287668 126960 42RYFAAXX_2 199112 73119 140234 224647 2859 482728 154222 42RYFAAXX_3 199754 54814 229473 167783 966 328480 106565 42RYFAAXX_4 153972 48697 117009 108928 4524 459772 82452 42RYFAAXX_5 213663 81749 171561 125466 23494 638285 111861 42RYFAAXX_6 223904 158701 216016 182990 15088 2352728 304136 42RYFAAXX_7 43960 20390 48778 50633 2990 1601294 358798 42RYFAAXX_8 114184 76460 161766 112155 3963 1418636 331269 42TA8AAXX_1 209504 110403 202939 170848 9397 1172234 29654 42TA8AAXX_2 247169 129395 241152 199778 11081 1370834 35377 42TA8AAXX_3 234874 122669 229713 188259 10421 1276791 34617 42TA8AAXX_4 7536 3825 7491 5993 286 35775 1186 42TA8AAXX_5 268255 142184 256195 219089 12736 1578967 36864 42TA8AAXX_6 276851 152735 241299 233912 16134 2055548 28646 42TA8AAXX_7 248149 130404 245678 200219 10514 1323804 36707 42TB9AAXX_1 396319 179265 325335 371466 24609 1225522 117300 42TB9AAXX_2 208997 80218 203743 193321 10447 581403 1227507 42TB9AAXX_3 322074 172149 328517 353218 18128 1714080 194007 42TB9AAXX_4 169764 92303 176972 176781 9923 522691 75863 42Y6WAAXX_6 258018 139150 266010 266081 14942 798382 108805 42TB9AAXX_6 481760 165996 328618 392708 17353 1309491 110620 42TB9AAXX_7 318764 180795 338405 380984 18276 1466092 139352 42TBWAAXX_1 174843 41078 122740 134525 5348 7476669 463671 42TBWAAXX_2 251776 117276 290676 297507 5228 2656337 96529 42TBWAAXX_3 263428 56732 374444 239685 2803 6108846 246493 42TBWAAXX_4 258983 109397 266951 288764 7738 4248023 71767 42TBWAAXX_5 194563 79854 242619 178498 3211 6974108 144065 42TBWAAXX_6 134492 69385 154278 141167 2070 2600381 110271 42Y6WAAXX_1 152163 78823 176127 160536 2273 2905347 126052 42TBWAAXX_7 183667 85704 237702 189840 2334 1577196 40273 42TBWAAXX_8 247824 59145 247057 213437 9842 5931445 161764 42TCBAAXX_1 238697 66651 213395 159981 2406 2465923 53836 42TCBAAXX_2 343158 44343 224613 244119 2275 4991631 186525 42TCBAAXX_3 202888 61467 175334 175424 7260 6344389 150794 42TCBAAXX_4 250931 89260 262811 265846 7913 1979162 115526 42TCBAAXX_5 346214 109441 303047 252941 62244 2027256 73368 42TCBAAXX_6 102369 37626 89193 96184 926 5156736 64094 42TCBAAXX_7 162829 55426 137376 144250 11463 950266 24830 42TCBAAXX_8 169038 66814 156278 172536 2439 600552 40208 42TCLAAXX_1 35214 14555 47234 49727 194 151194 3617 42Y39AAXX_2 286920 123459 340597 420782 1578 1504861 20725 42TCLAAXX_3 33503 13123 36969 46820 204 205823 4730 42Y39AAXX_5 300086 121717 288755 432597 1947 2200704 28989 42TCLAAXX_4 95968 38823 98256 121607 429 475967 9926 42Y39AAXX_6 278583 122949 247475 390709 1757 1761838 17979 42TCLAAXX_5 87059 32563 86535 93487 508 525589 12162 42Y39AAXX_7 309586 121273 259073 359794 2006 2539693 26110 42TG0AAXX_2 89555 39363 121935 94006 555 822062 45624 42TG0AAXX_3 337006 102567 224466 275071 4184 1968681 76644 42TG0AAXX_4 317211 132199 201538 285796 11463 1865626 107016 42TG0AAXX_5 160310 58797 163245 166896 2742 2133218 42712 42TG0AAXX_6 180374 66758 178252 198820 11046 3361874 59543 42TG0AAXX_7 4622 1745 4114 14065 732 10887925 239684 42TG0AAXX_8 238090 81509 210813 249715 17286 4144713 114865 42Y2MAAXX_1 314788 122954 286915 411080 1449 1119573 72575 42Y2MAAXX_2 342536 150475 257493 385614 852 1070738 57116 42Y2MAAXX_3 336717 131263 272622 423931 1480 1222218 53357 42Y2MAAXX_4 385161 188089 303151 438286 836 780280 32347 42Y2MAAXX_5 315167 129257 368062 427431 45084 967259 44119 42Y2MAAXX_6 311769 141127 295019 361097 32843 1385788 80079 42Y2MAAXX_7 297947 150482 347648 415776 39710 501461 44323 42Y2MAAXX_8 353037 175982 319235 377274 27713 1816186 107616 42Y39AAXX_3 318630 124611 345702 389291 1366 1497457 38382 42Y39AAXX_4 317502 125039 339426 391111 1354 1524817 36345 42Y6NAAXX_1 310148 105905 225357 351762 2037 1989445 65003 42Y6NAAXX_2 255610 112697 236814 282913 3002 1205222 43781 42Y6NAAXX_4 241813 107323 198062 345580 1755 1333802 52963 42Y6NAAXX_5 263562 110352 188811 314962 1741 2063447 47860 42Y6NAAXX_6 391444 81453 238663 274634 3171 1604541 60637 42Y6NAAXX_7 240630 79129 154442 394201 8730 1388814 45287 42Y6NAAXX_8 372036 153750 247142 373102 1871 1078869 48294 42Y6WAAXX_2 249661 80034 234127 218570 9870 225673 48769 42YMTAAXX_2 174158 56541 160917 154591 7244 163951 33809 42Y6WAAXX_3 310337 127874 349747 230248 15457 987906 91555 42YMTAAXX_4 141522 57992 160871 104253 6950 448005 44533 42Y6WAAXX_4 141372 86675 181038 139530 8252 3813971 171286 42YMTAAXX_8 76869 47101 99366 74503 4367 2048530 98007 42YMMAAXX_1 255209 118536 189888 318321 9170 1095200 41874 42YMMAAXX_2 456618 122574 352985 281578 8191 483556 46089 42YMMAAXX_8 436524 115533 356775 263380 6689 466182 43423 42YMMAAXX_3 460613 126702 253002 349039 3808 849766 39777 42YMMAAXX_4 300088 84040 266106 280756 11015 1013275 260335 42YMMAAXX_5 302870 138589 333931 388333 2888 1074957 99908 42YMMAAXX_6 282431 142583 314868 295993 20586 779333 526104 42YMMAAXX_7 320296 182451 248118 314541 23197 2797580 253615 42YMTAAXX_1 311197 76479 251236 288520 3717 282116 93455 42YMTAAXX_3 183338 85984 194383 171929 3546 1021747 107333 42YMTAAXX_5 261792 58340 101786 145663 3582 685778 106127 42YMTAAXX_6 377757 112265 280575 286452 1733 765014 258043 42YMTAAXX_7 169189 91632 147810 192700 604 621748 145760 43336AAXX_1 618869 283080 362368 885436 90951 890 4047 43336AAXX_2 779708 288848 629839 748113 63187 1269 9501 43336AAXX_3 615815 281066 323519 1898801 6057 1002 3566 43336AAXX_4 654494 283095 430670 1571822 6153 1817 2583 43336AAXX_5 613247 308861 362738 830697 204269 6366 19808 43336AAXX_6 592488 285012 272413 1052620 96495 1212 4063 43336AAXX_7 260886 122702 261558 278060 2193 3328173 427183 6137KAAXX_3 467505 175038 280504 545058 13898 1223990 788992 6137KAAXX_4 467309 175095 279192 543194 13939 1221633 803870 6137LAAXX_6 113573 49086 68793 113658 5050 182463 567284 6137KAAXX_6 495606 204129 294744 433045 5770 2679545 68438 6137KAAXX_7 644920 142191 489232 465857 18150 1630996 92026 6137KAAXX_8 413516 176516 361589 579628 1343 1827394 15836 6137LAAXX_7 248771 149999 118895 340837 65823 28396 65860 6137LAAXX_8 183526 105456 100667 232851 49008 18636 56496 61VFCAAXX_1 344817 184698 355025 473833 6429 2379159 420074 61VFCAAXX_2 343380 172365 349709 524423 7125 3636767 161470 61VFCAAXX_3 367218 179235 380369 481946 5388 2110933 84819 61VFCAAXX_6 407732 188260 412884 447411 13931 2327370 160521 62837AAXX_1 503729 269743 473051 583119 16923 1736659 107376 62837AAXX_2 461685 240696 435487 716066 1675 2233592 91061 62837AAXX_3 518636 220242 465628 674984 32060 1858618 27720 62837AAXX_4 454738 274093 405522 535531 19610 1480970 121512 62837AAXX_7 157455 71272 150237 162020 8868 226572 148401 62837AAXX_8 430193 184469 400194 520796 618 1262058 86580 6286PAAXX_1 466938 193877 468828 554183 20912 1576246 64497 6286PAAXX_2 431045 215647 431944 581655 1070 989915 75219 6286PAAXX_3 552869 176266 372616 641057 4679 2595818 196313 6286PAAXX_4 592530 133490 315300 510413 3370 2214274 206418 6286PAAXX_5 431870 140016 389672 427996 2534 3039154 291790 6286PAAXX_6 682128 187201 443613 497200 14922 2392482 162800 6286PAAXX_7 573423 200417 404063 754742 3864 2295990 241257 6286PAAXX_8 390526 177412 604225 529005 21529 1366406 187409

TABLE 3 Ψ-Chromosomal Ψ- Bladder Breast Cervical Colon Gastric Kidney Lymphoblastoid Melanoma Region Name Encode Yale (17) (64) (8) (6) (25) (12) (19) (10) chr21: 10202689-10203575 EIF3F manual proc 2 chr10: 37636369-37640031 ATP8A2 manual 6 chr10: 37640002-37644728 ATP8A2 manual 5 chr4: 141781899-141782720 KIAA1856 dup 4 chr10: 37666189-37668498 TMEM161B manual proc 4 chr19: 12531356-12532856 PGK1 manual dup 3 chr22: 23438167-23438592 CRIP1 manual proc 3 chr9: 75280000-75280934 DPP3 manual proc 3 chr10: 37619903-37620019 ATP8A2 manual 2 chr10: 37580608-37581341 ATP8A2 manual dup 2 chr10: 37577033-37577556 ATP8A2 manual dup 8 chr10: 37590732-37594328 ATP8A2 manual dup 6 chr1: 109447342-109448872 PCBP1 manual dup 2 chr2: 131895157-131898651 GNAQ manual proc 2 chr8: 130810585-130813055 MTRF1L dup 2 chr5: 92250781-92251791 CCT7 auto proc 2 chr7: 138533692-138534485 FCF1 manual proc 2 chr17: 44331639-44331679 RHOB dup 2 chr12: 12243007-12245031 MORF4L1 dup 2 chr1: 234516058-234516726 FKBP3 manual dup 2 chr14: 53527463-53528434 ATP5C1 manual proc 2 chr10: 69180083-69181213 AKR1B10 manual proc 2 chr8: 26461161-26461703 PSME2 proc 4 chr2: 152955000-152955599 NUDC manual proc 3 chr7: 134463620-134464973 RNF14 manual proc 2 chr10: 121746618-121747198 NACA manual proc 2 chr1: 218507681-218508028 AURKA manual proc 7 chr3: 115431891-115434722 KIAA1539 proc 4 chr3: 120732546-120733113 CSRP2 proc 4 chr2: 201985004-201986130 SCYL2 manual proc 4 chr2: 231530573-231530995 FAM36A manual proc 4 chrX: 110747689-110749928 EIF4B manual proc 4 chr10: 75852293-75853672 RAB5C manual proc 4 chr15: 81278450-81278844 BC117556 auto 3 chr19: 40565000-40566763 EEF1A1 dup 3 chr4: 135468269-135469814 PES1 proc 3 chr10: 31689689-31689904 SPTLC1 manual frag 3 chr1: 202765009-202765499 PEF1 manual proc 3 chr10: 75957261-75958035 MRPL35 manual proc 3 chr8: 48152971-48153133 A26A1 dup 2 chr15: 81288859-81289520 BC117556 auto 2 chr12: 31355668-31356398 SLC25A13 dup 2 chr11: 85683591-85684437 SET proc 2 chr4: 185717093-185717964 NOLA1 proc 2 chr4: 100049539-100049960 TBCA proc 2 chr5: 126875001-126876506 HNRNPK proc 2 chr12: 92041871-92042457 NACA proc 2 chr2: 149346124-149347002 USP8 manual frag 2 chr7: 53822238-53822358 ATM manual frag 2 chr4: 93322413-93324234 PMPCA auto proc 2 chrX: 119227888-119229412 EEF1A1 manual dup 2 chr1: 117985009-117985810 VDAC2 manual proc 2 chr17: 59917896-59918632 ATP5J2 manual proc 2 chr21: 15051843-15053508 POLR2C manual proc 2 chr9: 139655582-139655864 SET manual proc 2 chr18: 41862332-41864360 UTP18 proc chr1: 54763083-54763321 TALDO1 manual frag chr22: 28770926-28773344 CNN2 manual proc chr3: 37151088-37151663 UBE2D3 manual proc chr15: 69242617-69244956 HMGB1 proc chr12: 31798916-31799483 IFITM2 proc chr12: 8555270-8556510 SUPT4H1 proc chr12: 64915002-64915315 RBMS1 auto proc chr19: 59424557-59425022 LSM14A manual dup chr1: 144988906-144990026 IGF2BP2 manual proc chr14: 68403267-68404827 BLZF1 dup chr19: 56731589-56731634 FAM107B dup chr12: 21491749-21494398 TCEB1 dup chr1: 222429477-222430009 ZNF706 manual chr8: 55597596-55598332 SEC11A auto proc chrX: 136350864-136351728 RAC1 manual proc chr1: 84482546-84483186 NEDD8 manual proc chrX: 152525161-152526553 MRFAP1 manual proc chr19: 59469095-59469457 ORAOV1 dup chr14: 68405160-68406719 BLZF1 dup chr11: 124182827-124183139 RNF181 proc chr12: 114514705-114515025 UBA52 proc chr10: 22554510-22555015 PSME2 manual frag chr13: 97437263-97437450 FTL manual frag chr2: 26225408-26227645 SMARCE1 manual dup chr4: 84387420-84388630 AMT auto proc chr13: 42405938-42406759 ZDHHC4 manual proc chr9: 96088678-96089876 VDAC1 manual proc chr6: 149475018-149475620 SNRPB2 manual proc chr1: 245420770-245420911 ZNF430 manual proc chr22: 22040076-22042678 CES7 manual chr15: 19267708-19269952 CXADR auto proc chr22: 22031558-22032127 CES7 manual chr18: 54508763-54509828 MRPL37 proc chr4: 166544280-166544941 HADHA proc chr11: 18573250-18574450 MTCH1 proc chr10: 104925212-104926869 MARCKSL1 manual proc chr15: 33377487-33379076 RBM17 proc chr2: 132075527-132076801 AY458019 manual chr12: 118116932-118118276 PDAP1 auto proc chr7: 63665694-63668112 LOC402665 manual proc chr15: 19391669-19394059 NF1 dup chr15: 19396218-19399993 NF1 dup chr4: 72385029-72386725 SLC35A4 proc chr4: 140255185-140256207 PPP1R14B proc chr11: 125442528-125444160 NAP1L1 proc chr12: 60911988-60914886 KLF17 proc chr8: 48666667-48667924 UBE2N proc chr5: 75410408-75411560 SMS proc chr10: 93965940-93966789 NOLA2 manual chr12: 17033298-17034633 SKP1 proc chr19: 63029371-63030025 FKBP1A proc chr3: 121508215-121509682 PTOV1 proc chr3: 52741566-52743049 ZNF610 proc chr2: 94890365-94894064 LOC389834 proc chr1: 245430003-245432118 ZNF720 manual frag chr2: 69678006-69679772 B3GALNT1 manual dup chr22: 16277647-16279389 TERF2IP manual dup chr3: 132029176-132030005 GSTO1 auto proc chr14: 19216101-19218960 USP10 auto proc chr2: 54131611-54132922 HMGB1 manual proc chrX: 18793802-18794774 CCDC5 manual proc chr20: 25027736-25029870 VTCN1 manual proc chr10: 104595191-104596503 PTGES3 manual proc chr6: 101085019-101087991 DCUN1D1 manual proc chr20: 44525241-44526750 MKRN1 manual proc chr10: 46552660-46554269 HNRNPA1 manual frag 5 1 chr1: 174850424-174852903 PTP4A1 manual proc 2 1 chr9: 33592667-33595028 KIAA2015 proc 1 chr22: 22386358-22389509 GUSB manual 1 chr1: 47081250-47081689 CYP4Z1 manual proc 4 6 chr20: 32295708-32298037 DENR manual proc 2 chr8: 30225003-30227051 TAGLN2 auto proc 2 5 chr1: 145020394-145021949 SSB manual proc 2 chr13: 44066841-44068205 SMARCE1 manual proc 2 chr1: 176981907-176983662 PTPN2 manual proc 1 6 chr4: 113966768-113968338 TAF4B auto frag 4 chr13: 76456888-76460017 DHX9 manual proc 4 chr12: 8177240-8178828 POU5F1 auto proc 1 chr9: 5103911-5104767 IGHE manual proc 1 chr17: 30840954-30844887 E2F3 proc 2 chr5: 31945012-31947315 TPT1 auto dup 1 chr5: 102395954-102396670 EIF3K auto proc 1 chr9: 5075006-5076284 PDSS1 manual proc 2 chr15: 87332965-87334484 CAPZA2 proc chr12: 4613400-4615020 RAB5A dup chr12: 9199537-9200023 TPT1 proc chr1: 70157624-70158591 PIN1 manual proc chr3: 12344333-12344751 PFDN1 manual proc chr11: 77772536-77773641 ZNF75D proc 1 chr5: 172121628-172124841 FAM58A auto proc 1 chrX: 64605779-64607158 AP1M2 manual dup 2 chrX: 91255170-91255864 EIF4A1 manual proc 2 chr2: 162640152-162642586 TIMM8A manual proc chr4: 166545018-166547102 HADHA proc chr22: 34623087-34624393 NDUFA9 manual proc 1 chr1: 177822521-177824924 CENTG2 manual proc 3 chr9: 75278688-75279979 DPP3 manual proc 3 1 chr9: 37625488-37627344 RAB1B manual 3 chr15: 98905757-98909660 PRKY auto 2 chr13: 29768191-29769131 PRDX2 manual proc 2 1 chr17: 6771934-6772425 SPIC proc 3 1 chr7: 55294166-55295027 CALM1 manual proc 2 chr14: 20065201-20066879 SET proc 2 1 chrX: 61915436-61916582 SSB manual proc 2 1 chr14: 57820991-57822278 HMGB1 auto proc 2 chr11: 47882316-47883972 SEC61B proc 2 1 chr3: 198845497-198847337 PPP4R2 dup 1 chr1: 38947029-38949502 HSPA5 manual proc 1 chr6: 38663042-38664706 TFG manual proc 2 2 chr5: 144588471-144590025 ASS1 auto proc 1 2 chr12: 6865020-6866674 DSTN manual 1 2 chr1: 81740357-81744083 ARID3B manual proc 1 2 chr8: 50815164-50816385 PSAT1 proc 1 2 chr2: 172056105-172057010 DAP3 manual frag 1 2 chr11: 118208607-118209718 SET auto proc 1 2 chr10: 120393399-120394061 TOMM22 manual proc 1 2 chr11: 86208209-86209928 MOBKL3 proc 2 2 chr3: 73060699-73061349 FTH1 proc 1 chr22: 22325000-22325556 ASL manual dup 1 4 chr3: 173800619-173804689 SLC31A1 manual proc 3 chr13: 19035415-19037296 CASC4 manual proc 1 3 chr4: 40482518-40483890 ARL4A proc 1 chr18: 53581850-53582535 MRPS17 proc 1 chr6: 1458119-1459994 ELF2 manual proc 1 chr21: 32790823-32791600 EXOSC3 manual proc 1 chr7: 46003545-46004373 FTL manual proc 2 1 chr13: 40464767-40464951 RGS17 manual proc 6 chrX: 46468751-46470028 CHMP5 manual proc 6 chr6: 90581057-90582594 FAM64A manual proc 4 chr22: 37448047-37449602 PRDX3 manual proc 3 chr19: 62378395-62379706 PTCD3 dup 2 chr5: 42501936-42504461 ZNF35 proc 2 chr15: 93200012-93201180 GLTSCR2 auto proc 2 chr11: 18643045-18644377 SFRS3 auto proc 2 chr2: 43761451-43762368 ZFP106 manual frag 2 chr6: 158577413-158579430 SRP72 manual dup 2 chr14: 60316280-60317538 MAD2L1 proc 1 chr3: 31470003-31472686 THRAP3 manual dup 1 chr9: 83890554-83893228 DDX10 manual proc 1 chr1: 246951416-246952125 AHCY manual frag 2 1 chrY: 5265643-5266973 EIF4A1 manual proc 2 1 chr12: 17035000-17036276 EEF1A1 proc 3 1 chr12: 6457164-6459964 PKP2 proc 8 chr2: 197835918-197836621 ATPSG2 manual proc 8 chr10: 118771731-118773667 DDX3X manual 1 chr13: 40465037-40465571 RGS17 manual proc 4 chr4: 103870768-103875031 MANBAL proc 3 chr13: 30025729-30027622 PTPN2 manual proc 3 chr10: 51695144-51697065 DYNC1I2 manual proc 1 chr5: 139941169-139942270 CCDC5 manual proc 1 chr2: 201982582-201984995 SCYL2 manual proc 6 chr2: 182267396-182268139 SAP18 manual proc 1 chr3: 133588073-133590018 KIAA1333 dup chr1: 202041181-202041985 CHMP5 manual proc 6 chr4: 83415253-83417203 BIN2 proc 1 chr18: 70208031-70208617 FAU proc 3 chr14: 30221784-30222571 UBE2C proc 2 chr7: 23625349-23630025 FCF1 manual dup 3 chr4: 24268370-24269026 ATP5L proc 1 chr17: 18752228-18753057 RANBP1 manual proc 1 chr6: 139701047-139702459 DNAJC7 manual proc 5 chr1: 2454300040-245431986 ZNF430 manual frag 1 chr3: 31197239-31199007 CNN2 manual proc 1 chr3: 138100000-138101718 RAD51AP1 auto proc chrX: 17026484-17028444 CBX1 manual proc chr3: 194779703-194779896 EEF1A1 manual frag 2 chr3: 32769304-32770026 SUGT1 manual proc 2 chr7: 25695625-25696086 UBA52 proc chr12: 110503660-110503886 IFITM1 proc 5 chr17: 18510983-18512998 FOXO3 manual chr22: 22070000-22074479 ZDHHC8 manual frag 1 chr17: 60205003-60209312 LOC201175 proc 6 chr3: 49329045-49329924 SSNA1 proc 3 chr22: 22045609-22049946 CES7 manual 1 chr2: 20355007-20355544 RP9 dup 1 chr15: 33171848-33172885 U2AF1 proc 1 chr7: 75540406-75544538 LOC285908 manual proc 1 chr5: 110312099-110314335 BCLAF1 dup 1 chr4: 119333317-119335028 FKBP4 proc 1 chr3: 171145011-171147501 FHL1 proc 4 chr2: 132196348-132197314 BC016035 manual proc 2 1 chrX: 70180396-70182077 SOCS5 manual dup 3 1 chr15: 36537765-36539186 CTDSP2 proc 2 1 chr1: 92311703-92313396 SET manual proc 2 1 1 chr15: 34696499-34699553 LARP4 proc 1 1 chr14: 74019321-74020027 RAP1A proc 1 1 chr14: 99902477-99903076 NDUFB3 proc 1 chr1: 97783716-97784986 SEC63 manual frag 1 chrX: 154170506-154173981 TWF1 manual proc 1 2 chr15: 57756054-57757383 PIGH proc 3 chr6: 145070172-145071408 NT5DC1 manual frag 1 chr5: 97575000-97575656 PSME2 proc 1 1 chr20: 5220061-5221727 UBE2D3 manual 1 1 chr9: 34906998-34908341 GLUL manual proc 1 1 chr7: 63005787-63008547 NMD3 manual proc 1 1 chr12: 46765022-46765808 ATP6V1F proc 1 chr5: 157345785-157347510 CDC37 auto proc 1 1 chr15: 32573790-32575001 FSCN1 proc 1 chr2: 139375038-139376849 AHCY manual proc 2 chr1: 64080787-64082020 CFL1 manual proc 1 3 chr19: 32986379-32989682 BC040831 proc 1 2 chr1: 238372430-238375019 PSMD2 manual proc chr10: 21357922-21359678 EIF4B manual proc 2 chr14: 57677677-57678048 UBA52 proc 3 1 chr16: 4552399-4553233 SUB1 proc 4 4 chrX: 36139141-36140020 HMGB1 manual proc 3 1 2 chr16: 51246583-51248855 TPM3 auto 3 2 chr3: 97550893-97552589 HNRNPK proc 2 1 chr6: 151297464-151299652 ARL4A manual proc 2 1 chrX: 62435062-62436548 CBX1 manual proc 2 2 1 chr7: 138506992-138509638 MSL3L1 manual dup 1 2 chr2: 204206408-204208995 ZNF207 manual proc 1 2 chr15: 49024038-49025027 WDSOF1 proc 1 2 chr7: 84495121-84497088 HSPA8 manual proc 1 2 1 chr17: 42855745-42858503 NFE2L3 dup 2 1 chr16: 17095569-17097803 LYRM2 dup 1 3 1 chr18: 22090016-22090564 FAM60A proc 1 3 chr9: 37875565-37875969 TXNDC14 manual proc 5 4 chr11: 17030098-17030554 MGC72080 auto proc 3 3 chr4: 68265004-68266433 ST3GAL1 auto proc 2 1 chr1: 16890145-16890316 PDE4DIP manual 2 1 chr5: 108257676-108258248 LSM2 proc 1 1 chr4: 174790868-174792152 RAN manual proc 1 1 2 chr1: 87282633-87284966 UBA2 manual frag 1 1 2 chr12: 40966857-40969856 IGF2BP2 auto proc 1 1 3 chr3: 187961542-187964137 PSMD10 manual proc 1 1 5 chr7: 16870050-16872687 RAD17 manual proc 3 3 chr11: 82597892-82598941 CKS1B proc 1 3 2 chrX: 138942285-138943083 HNRNPA3 manual proc 1 3 1 chr8: 120561397-120562903 ZNF532 auto frag 1 1 chr15: 100135383-100137014 FLJ00278 dup 3 1 chr11: 16461350-16462832 AKR1B1 auto proc 1 1 2 chr11: 29253864-29254659 EEF1A1 proc 1 3 chrX: 73296169-73299018 MKRN1 manual proc 1 3 chr2: 25932706-25933414 ENO3 manual frag 1 1 chr6: 143853283-143854931 VDAC1 manual proc 1 7 chr1: 42738096-42738591 TMSB4X manual 1 1 5 chr13: 98665103-98666182 H2AFZ manual proc 4 chr10: 13238600-13239995 BTBD7 manual dup 2 3 chr1: 104417120-104419481 THAP3 manual proc 1 2 chr14: 91136604-91139705 POLR3G proc 1 1 chr3: 73314742-73314982 CCDC75 auto proc 2 1 1 chrX: 40578772-40580026 MKRN1 dup 1 2 1 chr4: 136186068-136187470 EEF1A1 dup 3 1 chr9: 5100700-5103470 TCF3 manual proc 1 7 chr18: 27796204-27798261 PGD auto proc chr14: 70866169-70867395 PDZD11 proc 7 chr19: 21725455-21727418 CCNYL1 proc 1 8 chr1: 218865561-218868015 HDAC1 manual dup 3 chr17: 55317138-55317916 NDUFB8 proc 1 chr7: 7986381-7988620 PPIL4 manual dup 12 chr20: 31962213-31964566 TPM3 manual dup 2 1 chr2: 32280035-32282728 DDX50 manual dup 5 chr13: 21002739-21003960 FNTA manual proc 1 2 chr7: 156680057-156683908 UBXN2B manual dup 1 1 chr5: 67490784-67491620 EEF1B2 auto proc 1 1 chr10: 64650560-64652770 TATDN1 manual proc 4 chr19: 23100389-23102504 SNX6 proc 1 1 chr5: 72327995-72329739 DULLARD proc 6 chr13: 19542116-19543366 KRR1 manual dup 1 2 chr9: 107325071-107329784 GARNL1 manual dup 1 2 chr10: 65061132-65064798 MRPL35 manual proc 1 chrX: 72660041-72662733 MAP2K4 manual proc 1 chr6: 139012261-139013805 MTCH1 manual frag 2 chr1: 40371010-40373921 OAZ1 manual proc 3 chr10: 121370445-121373045 RAD1 manual proc 1 2 chr20: 32452814-32454340 CDC42 manual proc 2 chr12: 100881924-100882389 NENF proc chr14: 81452361-81454170 EIF3EIP proc 2 2 chr12: 70530011-70530466 MRS2 proc 1 3 chr2: 231145010-231146919 TPM3 manual proc 3 chr7: 56602283-56604066 YWHAE manual dup 2 1 chr5: 92628780-92629995 POLD2 auto proc 2 2 chr10: 66255316-66256651 ANXA2 manual proc 2 chr1: 16882259-16884855 EIF1AX manual 1 chr15: 19186009-19190031 PAK2 auto proc 4 chr4: 129295826-129297562 FOSL1 proc 3 chr17: 60204622-60205031 LOC201175 proc 2 chr1: 201002645-201003292 COX7C manual proc 2 chr8: 87563050-87564438 NTAN1 auto dup 1 1 chr13: 18425000-18427904 PHF2 manual dup 1 2 chr7: 63832277-63834664 MPZL1 manual proc 1 3 chr15: 19270058-19270354 CXADR auto proc 1 chr7: 98435001-98435457 RNF14 manual proc 5 chr9: 96300008-96304864 LMLN manual dup 2 chr16: 21692-25029 IL9R manual dup 1 4 4 chr21: 36588933-36589981 SFRS9 manual proc 1 3 1 chr4: 68263271-68265012 ST3GAL1 auto proc 1 2 1 chr5: 108413260-108415011 GJA1 6 1 1 chr7: 80128544-80129812 TFDP1 manual frag 1 1 chrX: 149149690-149150027 XRCC6 manual proc 2 1 chr17: 71733295-71734754 ATF4 manual 2 1 chr5: 108147697-108149170 GNB2L1 dup 1 chr4: 46420373-46421380 RAC1 auto proc 1 1 chr17: 73665057-73666771 EIF5A proc 1 1 1 chr7: 104957816-104958449 RNF181 proc 3 1 1 chr11: 122335815-122337882 ATP5F1 proc 1 1 1 chr22: 23903543-23904988 STMN3 manual proc 11 1 chr17: 22433702-22435031 TUFM proc 3 1 chrX: 114805474-114806874 ASS1 manual proc 1 3 2 1 chr17: 26359119-26359614 YWHAE dup 2 1 3 chr15: 7919666 ANP32B auto proc 2 2 1 chr13: 28070998-28072283 EIF4A1 manual proc 2 1 1 1 chr6: 31351298-31355026 USP8 manual proc 1 1 3 chrX: 70176246-70179958 SOCS5 manual dup 1 1 chr3: 25771373-25774090 TAF9B manual proc 1 3 chr19: 14042134-14043294 EEF1D auto frag 7 1 chrX: 49283282-49284875 VDAC1 manual proc 1 3 1 chr22: 39511857-39515009 RFK manual proc 2 4 3 chr6: 138067402-138069986 PTPN11 manual proc 1 3 1 chr3: 197148302-197149669 PPP4R2 manual dup 3 2 2 chr17: 72157677-72159762 PTMA auto 3 3 5 4 chr5: 95130415-95132592 HSPD1 proc 3 3 2 chr2: 91318683-91319881 IGSF3 manual 1 2 1 1 chr6: 30707737-30709987 PTMA manual 1 2 2 chrX: 135716676-135717846 RAN manual proc 1 1 2 chr17: 25951505-25952090 SMURF2 manual 2 1 1 chr6: 30107367-30109699 ETF1 manual dup 1 2 chr16: 16366198-16368408 PKD1 dup 1 2 2 1 chr13: 76460074-76462820 DHX9 manual proc 1 1 6 chr22: 40726971-40728762 SLC25A5 manual proc 1 1 chr3: 123862123-123865031 EIF4B proc 1 2 chr6: 128942962-128943901 EEF1D manual proc 2 1 1 chr2: 202908139-202909954 FAM64A manual proc 1 1 3 chr13: 88810056-88813657 SP3 manual proc 1 1 1 4 chr13: 36410025-36411827 EIF4A1 manual proc 1 4 1 1 chrX: 120164368-120165004 HSPA8 manual 3 2 1 chrX: 70451371-70452584 ZCRB1 manual dup 1 2 2 chr7: 98432519-98435031 RNF14 manual proc 1 3 6 chr1: 78085216-78088009 CCDC55 manual proc 2 3 5 chr1: 152090703-152092464 ADFP manual proc 1 2 1 chr7: 137395348-137395688 TPT1 manual frag 2 1 chr11: 66285096-66286445 C1QBP auto proc 1 2 2 chr7: 127889632-127889961 MLL3 manual 1 2 1 chr1: 241495850-241498178 FCF1 manual proc 2 5 chr12: 74606217-74606813 TMEM141 proc 1 1 chr12: 78225570-78226943 REST dup 1 1 1 chr1: 169906030-169906835 PFN1 manual proc 1 6 chr2: 224277513-224278767 MLX manual proc 1 1 2 5 chr12: 64912853-64915025 RBM51 auto proc 1 2 chr19: 59425000-59426807 LSM14A manual dup 1 1 1 chr6: 36167532-36168612 NUDT5 manual proc 2 7 chr9: 70415029-70417781 DSE manual proc 1 1 4 chr15: 63850100-63851589 DNAJB14 auto proc 1 8 chr1: 203861013-203862993 GABARAP manual dup 1 1 chr6: 111285905-111288987 CNN2 manual proc 5 chr6: 36750047-36751612 LAP3 manual proc 1 1 chr3: 133590336-133594125 KIAA1333 dup 1 1 chr5: 172445309-172447866 CDC42 proc 4 chr7: 79844651-79844976 SNRPB manual frag 2 1 chr3: 76565834-76568498 CAP1 proc 1 1 1 chr12: 70528835-70530029 MRS2 proc 2 7 chr14: 69770604-69771489 FLJ00248 proc 1 1 chrX: 18269212-18269601 TMSB10 manual frag 1 1 1 chr3: 23895319-23895949 ARL4A manual proc 1 1 6 chr3: 155553099-155554758 DDX50 proc 1 2 2 chr2: 48712985-48713883 TPT1 manual proc 1 1 2 chr17: 78125786-78128688 ARL2BP dup 2 2 chr8: 124318219-124318608 UBA52 proc 3 chr14: 63130269-63131835 GCAT auto proc 3 6 chr9: 89871235-89875006 PNRC2 manual 2 2 chrX: 63570009-63572264 SHC1 manual proc 1 1 chr1: 245420253-245420689 ZNF720 manual proc 3 chr5: 21918407-21920011 HSPD1 proc 2 2 1 chr5: 31959147-31959652 TOMM7 proc 1 chr1: 164511305-164513491 EWSR1 manual dup 2 chr4: 66642565-66643009 IFITM3 proc 1 chr9: 33009522-33010029 LAGE3 manual proc 1 1 chr17: 10560021-10560742 MAGOH proc 1 2 chrX: 41420046-41420852 YWHAZ manual 1 1 7 chr2: 135985004-135986146 G3BP1 manual proc 1 3 1 2 chr16: 31486617-31488548 CSDA proc 3 1 chr12: 17034921-17035029 EEF1A1 proc 1 2 chr7: 143975043-143976509 EEF1A1 manual proc 2 1 2 1 chr7: 88106317-88107757 EEF1A1 manual proc 1 2 1 chr10: 21952707-21955029 HNRNPR manual proc 7 1 3 chr7: 117310724-117311343 SFRS3 manual 7 3 3 3 chr2: 41900352-41902242 LDHA manual proc 1 5 1 1 chr4: 4946239-4947833 LDHA auto proc 3 1 1 3 1 chr5: 114752657-114755023 CTNNA1 proc 1 3 1 5 1 chr4: 146516051-146518502 RTN3 proc 1 3 3 chr3: 174029034-174029700 ATP5G1 manual proc 1 2 1 1 1 chr4: 358246-359943 ZNF43 dup 2 1 2 chr5: 107088630-107089995 USP7 proc 2 1 6 chr4: 131043706-131044827 EEF1G proc 1 2 1 1 2 chr13: 28191258-28194994 CYP51A1 manual dup 2 1 2 1 2 chr2: 179027517-179028802 NUDC manual proc 1 1 2 1 chr15: 91140001-91141446 ASB9 proc 4 4 2 chr16: 46156547-46158361 EIF4B proc 3 1 2 chr3: 39375064-39376459 EEF1A1 manual proc 3 5 1 chr19: 1153449-1154923 HMGB2 auto proc 3 3 1 chr4: 110693368-110694731 SET proc 1 2 1 chrX: 115981067-115982444 SET manual proc 1 2 1 1 1 chr5: 37245024-37248385 OFD1 auto proc 1 1 2 7 chr4: 79320311-79322415 SERBP1 proc 1 2 1 3 chr22: 22600024-22604137 KLHL5 manual dup 2 2 1 chr5: 177330758-177333479 SUDS3 auto proc 2 2 chr8: 82692562-82693415 NIPA2 proc 1 1 1 chrY: 11781394-11785025 LOC389834 proc 1 1 3 chrX: 73266994-73269840 DDX3Y manual dup 1 1 2 chr16: 15137027-15139197 PKD1 manual dup 1 1 1 chr12: 1843255-1844894 LAMP1 auto proc 1 4 1 chr11: 119196989-119198204 BAT1 proc 6 6 8 6 chr6: 25131126-25132842 ASS1 manual proc 1 8 5 chr2: 152954216-152955031 NUDC manual proc 1 1 5 chr2: 25898653-25900030 PTGES3 manual proc 1 4 8 chr3: 97977193-97979955 CDV3 auto proc 1 2 5 chr3: 52382585-52384174 PPP2R5C proc 1 1 7 chr1: 245420126-245420978 ZNF682 manual proc 4 1 6 chrX: 73719066-73719697 PABPC1 manual frag 3 2 5 chr1: 212722108-212723497 AP3S1 manual proc 3 1 1 2 chr11: 92908039-92909143 SRP14 proc 2 3 chr21: 44290157-44291481 H2AFZ manual dup 1 2 8 1 chr1: 158906538-158909903 SET manual proc 1 2 2 7 chr12: 3820029-3825029 OTUD4 proc 1 1 5 chr14: 54835005-54835966 CHMP4B proc 3 2 4 chr15: 91077671-91078734 H2AFV auto proc 1 1 chr6: 147770007-147774161 YAP1 manual proc 2 2 chr8: 75677664-75679288 PCBP2 proc 1 1 1 chr6: 57002238-57004469 MRPL30 proc 1 1 1 chr19: 3821749-3823145 FTL auto proc 1 1 3 3 chr1: 245410530-245415024 PEX5 manual proc 1 2 2 chr17: 63602780-63604389 FBXO36 dup 2 1 chr5: 60223151-60223641 GNL3L manual 1 2 2 chr17: 18515359-18517127 FOXO3 manual proc 1 1 2 chr11: 129407907-129408375 TCEB2 proc 1 1 chr5: 68645003-68645660 CFL1 proc 3 2 chr5: 43530817-43532401 EEF1A1 proc 1 4 1 chr5: 14850010-14851722 RBBP4 proc 1 1 chr9: 130067782-130069317 FLJ00278 dup 1 1 1 chr9: 21685064-21689997 KHSRP manual proc 1 1 3 chr1: 226368927-226369874 FAM96A manual proc 2 1 1 2 chr13: 78381046-78382898 CCT5 manual proc 2 1 chrX: 75471475-75472671 LDHB manual proc 2 1 3 1 chr2: 236455494-236455892 TMSB10 manual proc 1 2 chr10: 76705756-76706390 HMGA1 manual 1 1 10 5 chr10: 79160515-79164753 ZNF532 manual dup 1 2 2 chr1: 97785042-97785538 SEC63 manual frag 1 1 chr7: 6647990-6650019 GZF1 manual 3 6 chr13: 18423767-18425026 PHF2 manual dup 1 1 2 chr19: 9746149-9746855 UBE2L3 proc 1 1 chr17: 20628146-20629946 SCD manual proc 9 1 2 chr1: 76938038-76939270 TPI1 manual proc 2 2 2 chr2: 162065731-162069847 AHCTF1 manual proc 1 2 1 1 chr1: 245429261-245429363 ZNF720 manual 2 1 5 chr22: 21935039-21937130 FBXW4 manual proc 1 1 3 chr19: 15881767-15883707 IPMK proc 3 1 1 2 chr2: 158630084-158632092 PTP4A1 manual proc 1 6 1 1 chr17: 24552608-24554860 TWF1 auto proc 1 6 3 2 1 chr7: 158107538-158109026 THAP5 manual frag 1 5 3 2 2 chr15: 88619130-88620026 PERP proc 15 4 2 2 chr18: 55835065-55835698 FAM60A auto proc 4 1 3 chr2: 84856616-84858887 LDHA manual proc 1 4 1 5 1 chr8: 62011957-62014951 NASP proc 1 3 6 1 chr9: 6656022-6660031 RNF2 manual proc 1 2 3 9 chr2: 91130114-91132611 TMEM128 manual frag 2 1 3 1 chr9: 6660006-6664836 RNF2 manual proc 2 1 1 2 8 chr11: 232267-233719 SRP19 dup 4 6 8 chr12: 74737397-74739842 DENR proc 7 6 1 15 chr6: 127717472-127720031 YWHAZ manual dup 2 1 5 3 1 chr16: 25046-28284 IL9R manual dup 1 1 5 3 chr8: 55046759-55049918 ESF1 proc 1 1 4 11 chr7: 56261370-56264649 CCNJ manual proc 1 3 1 4 chr15: 73400772-73402108 ANP32B proc 3 3 5 6 chr5: 175667341-175669888 BRCC3 dup 1 3 7 chr21: 36345013-36346248 FAM80B manual proc 1 1 2 2 chr2: 222535085-222537390 HSPA9 manual proc 1 2 2 1 2 chr7: 5566916-5567375 S100A11 manual proc 1 4 1 1 chrX: 130608331-130609932 HDGF manual frag 3 1 1 1 1 chrX: 113915399-113917620 HSPA8 manual proc 2 1 2 9 6 2 chr13: 27686701-27688179 EEF1A1 manual proc 1 1 3 4 chr8: 59500000-59502148 PTPN11 dup 1 3 1 9 chr17: 27578894-27579439 UBL5 proc 2 6 chr7: 30528821-30529744 FLJ00278 manual 1 1 8 chr11: 91708751-91709133 NDUFB11 manual proc 1 2 chr17: 20456347-20460008 DEF8 manual proc 1 1 6 chr11: 133498167-133500014 PTP4A2 proc 1 1 4 3 1 chr1: 207507608-207508364 ATP5G2 manual proc 1 5 chr16: 18386391-18389697 PKD1 dup 2 1 3 chr17: 27461314-27463910 WDR45L auto proc 1 1 4 chr10: 59642034-59642720 TPT1 manual proc 1 1 2 4 chr10: 94417431-94419676 EIF2S2 manual proc 1 2 6 1 chrX: 48519005-48520014 ACAA2 manual proc 1 3 4 chr9: 126952546-126954985 PRPS1 manual proc 6 1 1 4 chr9: 34308269-34310028 SERPINH1 manual proc 2 1 2 1 1 chr13: 48243346-48243963 PSME2 manual proc 2 3 5 chrX: 85225950-85227916 STIP1 manual proc 4 1 1 chr14: 95758990-95760012 CKS1B proc 2 4 2 chr4: 145986182-145988340 HSPD1 auto proc 2 3 3 1 chr7: 22516700-22518121 EEF1A1 manual dup 1 1 2 chr10: 43420007-43421764 CAP1 manual proc 1 2 1 chr17: 63634210-63634432 DQ587552 dup 2 2 1 chr12: 48067082-48070015 FGFR1OP2 proc 1 2 1 6 chr9: 138826841-138829981 NCL manual dup 2 2 1 chr10: 79210011-79211784 IMPDH1 manual proc 1 2 1 chr6: 109335327-109335840 ATP5J2 manual proc 1 2 2 3 chr1: 229223694-229225016 RNF4 manual proc 2 1 2 chr15: 34692846-34694996 TPM3 proc 1 2 1 1 chrX: 67920024-67922986 SERBP1 manual dup 3 1 1 4 chrX: 51683397-51683809 UCRC manual proc 1 3 chr6: 131545798-131548372 DPF2 manual proc 1 2 2 1 4 chr10: 135007719-135008625 BANF1 manual frag 1 1 2 1 2 chr10: 127345241-127346621 ALDOA manual proc 7 1 1 1 2 chr22: 19134094-19135031 KLHL12 manual proc 1 1 2 6 chr15: 43132056-43133113 YWHAZ proc 1 2 1 1 chr2: 106680143-106681581 EEF1A1 manual dup 1 1 1 4 1 chr12: 119766955-119768000 ARF1 auto proc 7 2 1 1 chr6: 53207834-53209186 HMGB1 manual proc 8 5 6 2 8 chr9: 30678968-30680030 RBMX manual proc 5 3 2 3 1 chr17: 64826385-64826952 SNRPG proc 4 3 1 13 chr7: 150830163-150832517 ETF1 proc 1 3 6 9 chr21: 38796179-38796358 SNRPG manual proc 1 2 5 7 1 3 chr1: 16885318-16888034 PDE4DIP manual 5 1 5 4 4 chr12: 99496386-99499915 PIGA proc 1 3 5 2 4 chr13: 44861259-44863071 RCN1 manual 1 3 3 2 chr9: 124488119-124489981 TLK1 manual dup 1 2 3 12 chrX: 65210128-65212872 EIF4B manual proc 1 1 2 1 5 chr15: 91139708-91140030 ASB9 proc 1 2 2 2 3 chr1: 166055742-166056259 FAM177A1 manual dup 3 1 2 8 1 chr9: 16765715-16765767 LSM1 manual proc 2 1 1 3 chr2: 171165069-171166985 HMGB1 manual proc 1 1 1 4 1 1 1 chr3: 157187740-157189549 SET proc 1 3 14 7 1 chr12: 19985423-19989724 TCP1 proc 1 1 6 2 2 chr9: 98527969-98529661 MKRN1 manual dup 1 1 1 2 3 chr7: 46005000-46007016 TTC4 manual proc 1 1 1 1 2 chr2: 85421131-85422577 PEBP1 proc 2 7 1 2 chr12: 86700634-86702602 MKRN1 auto proc 1 1 1 1 4 2 chr15: 97615266-97617895 HSP90B1 proc 1 2 1 1 chr13: 40090629-40094438 RNF6 manual dup 2 3 2 7 chr17: 30756783-30758835 DTWD2 proc 1 2 1 1 chr17: 4072185-4075029 RYK proc 2 1 1 1 7 chr19: 45140233-45141668 PRR13 auto 1 1 1 5 1 chr17: 30850001-30851322 TAF5L proc 1 2 2 4 8 chr2: 202772424-202775011 DAZAP2 manual proc 1 1 1 1 1 chr12: 109351042-109353797 HMGA1 proc 1 2 1 1 chr10: 75161319-75163908 DUSP8 manual proc 7 1 2 chr21: 46897231-46898445 DSTN manual frag 1 1 3 5 chr15: 54085179-54086686 CNOT6L auto proc 1 2 4 1 3 chr5: 25945144-25949126 MSN proc 1 4 1 chr3: 185226809-185228146 EEF1A1 manual dup 2 1 5 1 chr7: 20588278-20589374 EEF1A1 manual proc 1 1 3 1 chr3: 44595235-44597668 MPRIP manual dup 1 1 1 1 chr7: 39575135-39576400 TXNDC1 manual proc 4 2 3 6 chr1: 51395688-51396740 CFL1 manual proc 3 1 2 chr14: 64815693-64817730 PTBP1 auto dup 2 1 2 5 chr1: 16006265-16007067 UQCRH manual 1 4 2 chr5: 177525251-177526202 APOA1BP proc 5 2 1 3 chr1: 144990000-144992583 IGF2BP2 manual proc 2 2 3 1 1 chr7: 55672416-55674246 CDC42 manual proc 1 1 4 1 chr5: 114875647-114877498 CCT5 proc 1 3 1 1 chr2: 101256951-101257613 PPIA dup 2 1 3 8 chr7: 27462505-27465027 EIF4H manual proc 1 1 1 1 chrX: 100676203-100679915 PRKCI manual proc 1 1 3 2 chr3: 171262714-171264755 SETD8 proc 1 1 3 1 chr3: 52202197-52204001 ALDOA dup 10 1 2 1 chrX: 25573624-25574445 RANBP1 manual 3 8 5 4 9 1 chr2: 191565081-191567610 RAB1A manual dup 7 3 3 4 1 chrX: 53210000-53210656 SUV39H2 manual frag 2 1 7 5 2 10 chrX: 41417881-41420027 YWHAZ manual 1 1 6 2 3 5 1 chr5: 43622114-43624741 AMD1 auto proc 1 5 3 1 10 1 chr1: 218493241-218494999 MORF4L1 manual proc 4 3 5 1 6 chr3: 95276627-95278752 RBBP4 proc 4 1 7 6 2 13 chr6: 160051470-160055015 HNRNPH2 manual proc 2 4 5 10 7 chr12: 55190981-55193352 HSPD1 proc 4 5 3 4 7 2 chr3: 48272166-48273216 MRPS18A manual proc 1 1 1 5 12 chr11: 6465021-6467394 VDAC1 dup 2 2 5 1 12 chrX: 81638952-81640007 EIF3J manual frag 1 6 5 7 4 chr4: 118715123-118716642 NT5C3 manual proc 6 5 2 5 1 chr12: 110590068-110592654 PCNP auto proc 1 4 4 1 1 8 chr20: 48963622-48964977 PSMD10 manual proc 1 2 4 1 11 chr4: 22337134-22338823 CDC42 auto 1 2 4 2 1 6 1 chr11: 61895019-61899450 RCC2 proc 2 3 2 4 3 1 chr1: 52606731-52607671 PLA2G12A manual proc 1 5 3 4 chr19: 58005048-58009278 PABPN1 proc 1 1 1 2 3 3 6 chr4: 88053138-88055031 ARPC1A dup 1 3 12 6 1 chr17: 30848980-30850029 TAF5L proc 1 2 4 9 10 chr6: 30262288-30264297 PAIP1 manual dup 2 3 1 2 11 chr9: 119885003-119885562 TPT1 manual proc 1 2 1 5 chr12: 54660003-54663591 RAB13 auto 1 1 2 6 1 chr10: 70062143-70062538 FAM36A manual 1 1 1 3 2 2 chr12: 19500335-19502091 EEF1A1 proc 1 1 4 1 4 1 chr17: 39660007-39663513 SHC1 proc 3 1 2 chr12: 16442198-16445014 SUPT16H proc 1 2 2 1 1 chrX: 120165030-120166529 HSPA8 manual proc 2 2 2 1 4 1 chr15: 51016593-51017949 EEF1A1 proc 2 8 2 8 1 chr22: 40833082-40834984 OLA1 manual proc 2 3 1 3 chr12: 3818860-3819919 OTUD4 proc 3 5 5 3 5 chr2: 74498320-74499480 HMGA1 manual 1 1 1 5 2 6 chr2: 138761156-138762932 YWHAE manual proc 3 5 4 6 chr8: 30215043-30218410 HSPA8 dup 1 2 5 1 chr13: 64430032-64431456 LGMN manual dup 2 1 3 2 2 chr1: 96685035-96686396 EEF1A1 manual proc 1 2 1 3 1 chr10: 32840157-32840929 C1D manual proc 1 2 1 1 5 chrX: 65092271-65093777 RBMX manual proc 2 2 2 1 2 chr17: 2436284-2437919 EIF4A1 dup 1 3 1 1 3 1 chr2: 127030021-127032314 YWHAZ manual proc 1 3 1 3 2 1 chr15: 19190000-19191609 PAK2 auto proc 1 4 1 1 3 chr9: 22001477-22002779 UBA52 manual proc 4 3 2 2 5 1 chr1: 177437318-177437893 EIF4A1 manual frag 2 2 6 2 3 2 chr4: 98042943-98043372 COX7A2 auto proc 2 7 1 1 5 chr10: 107436038-107439382 YWHAZ manual proc 1 7 5 4 4 1 chr3: 15895007-15896926 IMPDH1 manual dup 1 4 3 1 2 1 chr7: 144911241-144912979 DPY19L4 manual proc 1 2 4 3 4 3 chrX: 44377591-44379921 CTF8 manual proc 3 1 6 6 8 1 chrX: 73340516-73344880 RAB11FIP1 manual proc 2 4 5 6 1 13 chr12: 67322298-67323260 ATP5H proc 1 6 6 1 1 16 chr7: 72033364-72034127 POMZP3 dup 1 1 6 4 4 1 chr1: 89067086-89067800 TCEB1 manual proc 2 3 6 6 3 16 chrX: 135755159-135758921 RAB28 manual proc 4 3 5 2 5 9 chr5: 68644250-68645023 CFL1 proc 1 1 1 5 1 5 chr21: 31920001-31923002 FBXW11 manual proc 2 3 3 3 2 4 5 chr22: 24373154-24375027 YES1 manual dup 2 3 1 1 9 13 1 chr22: 22320853-22325031 ASL manual dup 1 2 3 8 2 1 chr3: 53070978-53074165 SERBP1 proc 1 1 2 6 7 chr1: 89341252-89343268 PTGES3 manual 1 2 1 11 5 11 chr6: 86193656-86194482 TPT1 manual proc 2 2 4 2 8 2 chr4: 39650588-39652334 PABPC1 dup 1 2 1 1 3 5 1 chr3: 139081781-139083983 HSPA8 proc 2 2 1 6 1 chrX: 65635098-65636615 PKM2 manual proc 1 3 1 1 1 chr7: 10457157-10459773 HSPA8 manual proc 4 2 3 4 1 11 2 chr7: 151694812-151694991 PSPH proc 2 2 1 13 3 chr12: 4076871-4079190 HSPA8 dup 2 4 2 7 1 chrX: 13306389-13307499 GPX1 manual proc 1 4 3 1 1 2 chr14: 61368169-61368862 COX4I1 proc 1 8 6 1 3 chr10: 23465825-23468573 YWHAZ manual 1 6 4 6 3 1 chr3: 182442769-182443381 FAU proc 4 6 2 1 7 chr8: 107777994-107779579 TAGLN2 proc 1 3 2 1 1 5 chr1: 72512203-72513454 GDI2 manual frag 1 2 1 3 5 1 chr14: 35420023-35420673 EWSR1 proc 1 7 1 3 1 9 2 chrX: 79711705-79715004 HK2 manual proc 1 3 1 1 4 chr1: 245460000-245461944 HSPA8 manual proc 1 3 1 2 7 2 chr3: 27649231-27650012 TPM4 manual frag 3 1 1 10 5 1 chr16: 14920001-14923862 PKD1 dup 2 1 3 1 3 1 chr6: 158950293-158952897 TATDN2 manual proc 4 7 6 6 14 1 chrX: 70555627-70557712 PABPN1 manual proc 3 7 6 4 16 chr7: 32762364-32763505 DPY19L2P2 manual dup 2 7 6 13 7 1 chr19: 35220001-35221268 TAF9 auto proc 1 5 3 5 5 8 7 chr3: 122007401-122009653 NAP1L1 auto proc 1 8 5 5 11 1 chr3: 40612582-40613978 EEF1G manual proc 3 2 14 4 8 2 chr12: 41110881-41113477 FXR1 proc 1 1 8 6 2 1 13 chr1: 233967900-233969581 LDHA manual proc 1 5 1 2 2 13 4 chr9: 32935789-32937584 ASS1 manual proc 1 4 5 2 2 14 chr1: 106235172-106236952 MATR3 manual proc 4 4 5 2 4 10 1 chr20: 60947228-60948154 DPH3 manual proc 4 7 6 4 5 3 chr12: 51833223-51834834 EIF4A1 auto proc 3 4 7 2 8 3 chr12: 13046376-13049181 HTR7 proc 2 2 5 2 5 2 3 chr19: 14461030-14461871 SNRPG proc 1 3 7 5 4 1 chr7: 65525025-65526430 SKP1 manual proc 2 3 5 2 1 2 9 1 chr9: 88816231-88818084 CDC20 manual proc 1 4 3 1 1 3 chr3: 115086410-115088196 DULLARD auto proc 2 3 4 9 7 1 chr8: 48585762-48587345 NSFL1C proc 1 3 2 3 1 4 6 chr1: 240223113-240224419 CFL1 manual proc 1 3 2 2 1 6 1 chr3: 36783146-36785030 HSPD1 manual proc 1 1 1 3 2 1 1 1 chr1: 145141125-145143358 CCT8 manual proc 2 7 4 5 16 6 13 chr10: 71593210-71594625 CALM2 manual proc 3 10 8 6 8 6 4 chr7: 137738291-137739988 PTMA manual frag 3 7 6 18 5 14 3 chr22: 24375001-24378128 YES1 manual dup 2 9 8 4 12 1 9 chr9: 97948095-97950029 EIF4B manual proc 3 8 6 15 3 15 3 chrX: 115766164-115766603 PRPF4B manual frag 4 5 2 6 10 5 9 2 chr7: 104095351-104099270 EIF4B manual proc 1 1 8 6 9 2 13 3 chr12: 12155020-12156368 PTMA auto frag 1 1 8 6 12 4 13 2 chrX: 74880003-74883639 TTC3 manual proc 4 11 6 5 9 4 4 chr2: 61016549-61018625 NONO manual dup 2 2 7 6 5 1 14 chr6: 143705076-143706473 PARL manual proc 2 3 5 5 13 9 3 chr3: 48306896-48308964 FCF1 manual proc 1 3 2 5 11 6 10 chr17: 37935489-37939966 PTP4A2 proc 1 3 7 6 9 3 9 1 chr5: 96416174-96418578 SET auto proc 2 3 8 6 10 14 3 chr22: 29627969-29630029 EIF4H manual proc 2 3 6 6 3 10 6 1 chr1: 116875720-116878445 NAP1L4 manual proc 5 3 4 1 2 15 2 chr10: 120681594-120682842 LDHA manual frag 3 7 3 5 6 9 2 chr11: 18465871-18469227 YWHAB proc 1 1 3 4 4 3 12 2 chr9: 12962422-12963578 PRDX1 manual proc 2 3 8 5 4 1 2 chr9: 34911199-34912896 YWHAZ manual proc 2 1 8 5 10 2 8 2 chr17: 11959531-11959908 DYNLT1 proc 2 12 2 5 3 4 chr19: 18002173-18005024 CS proc 1 3 5 5 4 8 3 chr20: 17940242-17942547 PTMA manual 2 2 6 4 6 5 1 chr4: 74183155-74184968 HMGA1 dup 1 2 6 1 2 9 chr6: 144563059-144563906 TPT1 manual proc 1 2 1 6 3 10 chr7: 124460752-124462651 EEF1G manual dup 4 4 3 2 1 10 2 chr9: 14910713-14912555 LDHA manual proc 2 5 1 1 3 8 2 chr22: 30995341-30999218 CPSF1 manual proc 4 2 4 1 1 4 chr22: 24075369-24076698 PHF10 manual proc 1 1 1 5 1 8 chrY: 11770408-11775026 FLJ00219 dup 12 37 3 5 2 9 10 chr11: 43875453-43878110 SEC14L1 auto proc 11 7 6 8 5 16 3 chrX: 23003631-23004877 FAM3C manual 7 10 1 4 13 1 6 3 chr12: 32770077-32771796 NAP1L1 proc 2 4 8 6 7 9 16 1 chr1: 75980428-75983188 DLST manual dup 2 6 6 4 6 17 2 chr6: 74058239-74059970 EIF3E manual proc 2 2 5 2 9 7 13 1 chr18: 1350751-1353998 ATAD1 auto dup 3 4 6 5 12 6 3 chr17: 25420266-25421375 STX18 proc 4 9 1 4 5 2 5 chrX: 114843363-114844764 EEF1G manual proc 3 5 5 5 6 11 2 chr16: 11905084-11905547 COX6C proc 1 14 1 4 1 3 11 1 chr4: 10982554-10984464 RNPS1 proc 2 5 3 1 10 5 7 chrX: 30558147-30559009 FTL manual proc 1 1 3 3 9 4 8 1 chr12: 9283162-9284461 PTMA dup 2 1 8 6 10 2 11 1 chr16: 68346815-68349469 NONO proc 1 1 7 4 7 1 8 2 chr6: 5917621-5919864 PKM2 manual proc 8 5 1 3 1 4 2 chr5: 75708184-75708770 SNRPC auto proc 8 55 8 6 19 6 19 10 chrX: 74875425-74880031 TTC3 manual proc 4 28 7 6 19 12 12 6 chr17: 60176781-60178361 ASCC3L1 dup 11 30 6 6 18 12 13 2 chr11: 113145499-113147696 COX7A2L proc 3 37 7 6 15 7 12 5 chr2: 234438687-234440030 MSL3L1 manual proc 5 21 7 6 16 4 9 2 chr17: 63636429-63636974 DQ587552 dup 12 49 1 6 11 12 10 5 chr3: 117845959-117848342 BZW1 auto frag 12 20 7 6 23 2 15 7 chrX: 122077782-122079346 MRRF proc 3 27 8 6 18 9 11 5 chr2: 234440001-234441782 MSL3L1 manual proc 5 17 7 6 19 3 9 2 chr11: 33051914-33054815 PIGC auto proc 1 7 8 6 19 8 16 3 chr10: 42335001-42336262 ZNF37A manual dup 2 6 8 6 16 9 16 2 chr18: 12056629-12058570 SSBP4 dup 2 21 1 3 16 7 11 1 chr3: 180460196-180461897 LRRFIP1 proc 1 12 6 5 8 1 15 2 chr22: 19135000-19137681 KLHL12 manual proc 2 11 7 6 2 8 14 3 chr17: 60380103-60384663 SLC16A6 dup 1 5 7 6 4 8 13 2 chr20: 3952190-3953301 FTL manual 6 5 5 4 19 6 9 1 chr12: 6864001-6865025 DSTN manual proc 2 2 6 6 19 7 11 2 chr12: 62501627-62504537 PABPC1 proc 3 9 4 3 6 2 7 1 chr2: 132196980-132198589 TOMM40 manual proc 1 7 7 5 9 2 11 1 chr1: 114880845-114882611 PKM2 manual proc 1 12 5 5 5 6 10 4 Ψ-Chromosomal MPN Oral Pancreas Prostate Salivary Sub Tissue Region (9) (2) (28) (89) (4) Sample # type # Expression chr21: 10202689-10203575 2 1 Bladder chr10: 37636369-37640031 6 1 Breast chr10: 37640002-37644728 5 1 Breast chr4: 141781899-141782720 4 1 Breast chr10: 37666189-37668498 4 1 Breast chr19: 12531356-12532856 3 1 Breast chr22: 23438167-23438592 3 1 Breast chr9: 75280000-75280934 3 1 Breast chr10: 37619903-37620019 2 1 Breast chr10: 37580608-37581341 2 1 Breast chr10: 37577033-37577556 8 1 Breast chr10: 37590732-37594328 6 1 Breast chr1: 109447342-109448872 2 1 Breast chr2: 131895157-131898651 2 1 Breast chr8: 130810585-130813055 2 1 Cervical chr5: 92250781-92251791 2 1 Colon chr7: 138533692-138534485 2 1 Colon chr17: 44331639-44331679 2 1 Gastric chr12: 12243007-12245031 2 1 Gastric chr1: 234516058-234516726 2 1 Gastric chr14: 53527463-53528434 2 1 Gastric chr10: 69180083-69181213 2 1 Gastric chr8: 26461161-26461703 4 1 Kidney chr2: 152955000-152955599 3 1 Kidney chr7: 134463620-134464973 2 1 Kidney chr10: 121746618-121747198 2 1 Kidney chr1: 218507681-218508028 7 1 Lymphoma chr3: 115431891-115434722 4 1 Lymphoma chr3: 120732546-120733113 4 1 Lymphoma chr2: 201985004-201986130 4 1 Lymphoma chr2: 231530573-231530995 4 1 Lymphoma chrX: 110747689-110749928 4 1 Lymphoma chr10: 75852293-75853672 4 1 Lymphoma chr15: 81278450-81278844 3 1 Lymphoma chr19: 40565000-40566763 3 1 Lymphoma chr4: 135468269-135469814 3 1 Lymphoma chr10: 31689689-31689904 3 1 Lymphoma chr1: 202765009-202765499 3 1 Lymphoma chr10: 75957261-75958035 3 1 Lymphoma chr8: 48152971-48153133 2 1 Lymphoma chr15: 81288859-81289520 2 1 Lymphoma chr12: 31355668-31356398 2 1 Lymphoma chr11: 85683591-85684437 2 1 Lymphoma chr4: 185717093-185717964 2 1 Lymphoma chr4: 100049539-100049960 2 1 Lymphoma chr5: 126875001-126876506 2 1 Lymphoma chr12: 92041871-92042457 2 1 Lymphoma chr2: 149346124-149347002 2 1 Lymphoma chr7: 53822238-53822358 2 1 Lymphoma chr4: 93322413-93324234 2 1 Lymphoma chrX: 119227888-119229412 2 1 Lymphoma chr1: 117985009-117985810 2 1 Lymphoma chr17: 59917896-59918632 2 1 Lymphoma chr21: 15051843-15053508 2 1 Lymphoma chr9: 139655582-139655864 2 1 Lymphoma chr18: 41862332-41864360 7 7 1 MPN chr1: 54763083-54763321 5 5 1 MPN chr22: 28770926-28773344 5 5 1 MPN chr3: 37151088-37151663 5 5 1 MPN chr15: 69242617-69244956 4 4 1 MPN chr12: 31798916-31799483 4 4 1 MPN chr12: 8555270-8556510 4 4 1 MPN chr12: 64915002-64915315 4 4 1 MPN chr19: 59424557-59425022 4 4 1 MPN chr1: 144988906-144990026 4 4 1 MPN chr14: 68403267-68404827 3 3 1 MPN chr19: 56731589-56731634 3 3 1 MPN chr12: 21491749-21494398 3 3 1 MPN chr1: 222429477-222430009 3 3 1 MPN chr8: 55597596-55598332 3 3 1 MPN chrX: 136350864-136351728 3 3 1 MPN chr1: 84482546-84483186 3 3 1 MPN chrX: 152525161-152526553 3 3 1 MPN chr19: 59469095-59469457 2 2 1 MPN chr14: 68405160-68406719 2 2 1 MPN chr11: 124182827-124183139 2 2 1 MPN chr12: 114514705-114515025 2 2 1 MPN chr10: 22554510-22555015 2 2 1 MPN chr13: 97437263-97437450 2 2 1 MPN chr2: 26225408-26227645 2 2 1 MPN chr4: 84387420-84388630 2 2 1 MPN chr13: 42405938-42406759 2 2 1 MPN chr9: 96088678-96089876 2 2 1 MPN chr6: 149475018-149475620 2 2 1 MPN chr1: 245420770-245420911 2 2 1 MPN chr22: 22040076-22042678 9 9 1 Prostate chr15: 19267708-19269952 9 9 1 Prostate chr22: 22031558-22032127 6 6 1 Prostate chr18: 54508763-54509828 6 6 1 Prostate chr4: 166544280-166544941 4 4 1 Prostate chr11: 18573250-18574450 4 4 1 Prostate chr10: 104925212-104926869 4 4 1 Prostate chr15: 33377487-33379076 3 3 1 Prostate chr2: 132075527-132076801 3 3 1 Prostate chr12: 118116932-118118276 3 3 1 Prostate chr7: 63665694-63668112 3 3 1 Prostate chr15: 19391669-19394059 2 2 1 Prostate chr15: 19396218-19399993 2 2 1 Prostate chr4: 72385029-72386725 2 2 1 Prostate chr4: 140255185-140256207 2 2 1 Prostate chr11: 125442528-125444160 2 2 1 Prostate chr12: 60911988-60914886 2 2 1 Prostate chr8: 48666667-48667924 2 2 1 Prostate chr5: 75410408-75411560 2 2 1 Prostate chr10: 93965940-93966789 2 2 1 Prostate chr12: 17033298-17034633 2 2 1 Prostate chr19: 63029371-63030025 2 2 1 Prostate chr3: 121508215-121509682 2 2 1 Prostate chr3: 52741566-52743049 2 2 1 Prostate chr2: 94890365-94894064 2 2 1 Prostate chr1: 245430003-245432118 2 2 1 Prostate chr2: 69678006-69679772 2 2 1 Prostate chr22: 16277647-16279389 2 2 1 Prostate chr3: 132029176-132030005 2 2 1 Prostate chr14: 19216101-19218960 2 2 1 Prostate chr2: 54131611-54132922 2 2 1 Prostate chrX: 18793802-18794774 2 2 1 Prostate chr20: 25027736-25029870 2 2 1 Prostate chr10: 104595191-104596503 2 2 1 Prostate chr6: 101085019-101087991 2 2 1 Prostate chr20: 44525241-44526750 2 2 1 Prostate chr10: 46552660-46554269 6 2 Cervical, Gastric chr1: 174850424-174852903 3 2 Cervical, Gastric chr9: 33592667-33595028 2 3 2 Prostate, Cervical chr22: 22386358-22389509 2 3 2 Prostate, Cervical chr1: 47081250-47081689 10 2 Breast, Bladder chr20: 32295708-32298037 1 3 2 Colon, Prostate chr8: 30225003-30227051 7 2 Gastric, Breast chr1: 145020394-145021949 1 3 2 Gastric, Prostate chr13: 44066841-44068205 1 3 2 Kidney, Prostate chr1: 176981907-176983662 7 2 Lymphoma, Breast chr4: 113966768-113968338 1 5 2 Lymphoma, Prostate chr13: 76456888-76460017 1 5 2 Lymphoma, Prostate chr12: 8177240-8178828 9 10 2 MPN, Lymphoma chr9: 5103911-5104767 5 6 2 MPN, Lymphoma chr17: 30840954-30844887 5 7 2 MPN, Lymphoma chr5: 31945012-31947315 4 5 2 MPN, Lymphoma chr5: 102395954-102396670 4 5 2 MPN, Lymphoma chr9: 5075006-5076284 4 6 2 MPN, Lymphoma chr15: 87332965-87334484 3 1 4 2 MPN, Prostate chr12: 4613400-4615020 2 1 3 2 MPN, Prostate chr12: 9199537-9200023 2 1 3 2 MPN, Prostate chr1: 70157624-70158591 2 1 3 2 MPN, Prostate chr3: 12344333-12344751 2 1 3 2 MPN, Prostate chr11: 77772536-77773641 2 3 2 MPN, Lymphoma chr5: 172121628-172124841 2 3 2 MPN, Lymphoma chrX: 64605779-64607158 1 3 2 Breast, Oral chrX: 91255170-91255864 1 3 2 Lymphoma, Oral chr2: 162640152-162642586 1 45 46 2 Prostate, Pancreas chr4: 166545018-166547102 1 21 22 2 Prostate, Pancreas chr22: 34623087-34624393 13 14 2 Prostate, Breast chr1: 177822521-177824924 1 4 2 Breast, Prostate chr9: 75278688-75279979 4 2 Breast, Lymphoma chr9: 37625488-37627344 1 4 2 Breast, Pancreas chr15: 98905757-98909660 1 3 2 Breast, Prostate chr13: 29768191-29769131 3 2 Breast, Lymphoma chr17: 6771934-6772425 4 2 Cervical, Colon chr7: 55294166-55295027 1 3 2 Cervical, MPN chr14: 20065201-20066879 3 2 Cervical, Melanoma chrX: 61915436-61916582 3 2 Cervical, Melanoma chr14: 57820991-57822278 2 4 2 Cervical, MPN chr11: 47882316-47883972 3 2 Breast, Cervical chr3: 198845497-198847337 3 4 2 Prostate, Cervical chr1: 38947029-38949502 3 4 2 Prostate, Cervical chr6: 38663042-38664706 4 2 Colon, Gastric chr5: 144588471-144590025 3 2 Kidney, Colon chr12: 6865020-6866674 3 2 Lymphoma, Colon chr1: 81740357-81744083 3 2 Lymphoma, Colon chr8: 50815164-50816385 3 2 Gastric, Colon chr2: 172056105-172057010 3 2 Gastric, Colon chr11: 118208607-118209718 3 2 Gastric, Colon chr10: 120393399-120394061 3 2 Gastric, Colon chr11: 86208209-86209928 4 2 Gastric, Lymphoma chr3: 73060699-73061349 2 3 2 Prostate, Gastric chr22: 22325000-22325556 5 2 Kidney, Colon chr3: 173800619-173804689 2 5 2 Kidney, MPN chr13: 19035415-19037296 4 2 Lymphoma, Kidney chr4: 40482518-40483890 2 3 2 Prostate, Kidney chr18: 53581850-53582535 3 4 2 Prostate, Kidney chr6: 1458119-1459994 3 4 2 Prostate, Kidney chr21: 32790823-32791600 3 4 2 Prostate, Kidney chr7: 46003545-46004373 3 2 Gastric, Kidney chr13: 40464767-40464951 1 7 2 Lymphoma, MPN chrX: 46468751-46470028 1 7 2 Lymphoma, MPN chr6: 90581057-90582594 1 5 2 Lymphoma, MPN chr22: 37448047-37449602 3 6 2 Lymphoma, Prostate chr19: 62378395-62379706 1 3 2 Lymphoma, Prostate chr5: 42501936-42504461 1 3 2 Lymphoma, Prostate chr15: 93200012-93201180 1 3 2 Lymphoma, Prostate chr11: 18643045-18644377 1 3 2 Lymphoma, Prostate chr2: 43761451-43762368 2 4 2 Lymphoma, Prostate chr6: 158577413-158579430 2 4 2 Lymphoma, Prostate chr14: 60316280-60317538 2 3 2 Prostate, Lymphoma chr3: 31470003-31472686 2 3 2 Prostate, Lymphoma chr9: 83890554-83893228 2 3 2 Prostate, Lymphoma chr1: 246951416-246952125 3 2 Lymphoma, Melanoma chrY: 5265643-5266973 3 2 Gastric, Melanoma chr12: 17035000-17036276 4 2 Lymphoma, Melanoma chr12: 6457164-6459964 7 15 2 Lymphoma, MPN chr2: 197835918-197836621 7 15 2 Lymphoma, MPN chr10: 118771731-118773667 6 7 2 MPN, Cervical chr13: 40465037-40465571 5 9 2 MPN, Lymphoma chr4: 103870768-103875031 4 7 2 MPN, Lymphoma chr13: 30025729-30027622 4 7 2 MPN, Lymphoma chr10: 51695144-51697065 4 5 2 MPN, Cervical chr5: 139941169-139942270 4 5 2 MPN, Cervical chr2: 201982582-201984995 4 10 2 Lymphoma, MPN chr2: 182267396-182268139 4 5 2 MPN, Colon chr3: 133588073-133590018 3 6 9 2 Prostate, MPN chr1: 202041181-202041985 3 9 2 Lymphoma, MPN chr4: 83415253-83417203 2 3 2 MPN, Gastris chr18: 70208031-70208617 2 5 2 Breast, MPN chr14: 30221784-30222571 2 4 2 Lymphoma, MPN chr7: 23625349-23630025 2 5 2 Lymphoma, MPN chr4: 24268370-24269026 2 3 2 MPN, Cervical chr17: 18752228-18753057 2 3 2 MPN, Cervical chr6: 139701047-139702459 2 7 2 Lymphoma, MPN chr1: 2454300040-245431986 2 3 2 MPN, Colon chr3: 31197239-31199007 2 3 2 MPN, Colon chr3: 138100000-138101718 1 2 3 2 Prostate, MPN chrX: 17026484-17028444 1 2 3 2 Prostate, MPN chr3: 194779703-194779896 1 3 2 Lymphoma, MPN chr3: 32769304-32770026 1 3 2 Lymphoma, MPN chr7: 25695625-25696086 2 1 3 2 MPN, Oral chr12: 110503660-110503886 1 6 2 Gastric, Oral chr17: 18510983-18512998 1 2 3 2 Prostate, Pancreas chr22: 22070000-22074479 14 15 2 Prostate, Cervical chr17: 60205003-60209312 13 19 2 Breast, Prostate chr3: 49329045-49329924 9 12 2 Prostate, Breast chr22: 22045609-22049946 8 9 2 Prostate, Kidney chr2: 20355007-20355544 5 6 2 Prostate, Breast chr15: 33171848-33172885 5 6 2 Prostate, Breast chr7: 75540406-75544538 4 5 2 Prostate, Breast chr5: 110312099-110314335 2 3 2 Prostate, Breast chr4: 119333317-119335028 2 3 2 Prostate, Breast chr3: 171145011-171147501 1 5 2 Lymphoma chr2: 132196348-132197314 2 5 3 Cervical, Prostate chrX: 70180396-70182077 2 6 3 Colon, Prostate chr15: 36537765-36539186 1 4 3 Colon, Lymphoma chr1: 92311703-92313396 4 3 Colon, Gastric chr15: 34696499-34699553 2 4 3 Prostate, Breast chr14: 74019321-74020027 7 9 3 MPN, Cervical chr14: 99902477-99903076 6 1 8 3 MPN, Lymphoma chr1: 97783716-97784986 5 1 7 3 MPN, Lymphoma chrX: 154170506-154173981 5 8 3 MPN, Lymphoma chr15: 57756054-57757383 5 3 11 3 MPN, Lymphoma chr6: 145070172-145071408 3 1 5 3 MPN, Lymphoma chr5: 97575000-97575656 3 5 3 MPN, Gastric chr20: 5220061-5221727 3 5 3 MPN, Gastric chr9: 34906998-34908341 2 4 3 MPN, Breast chr7: 63005787-63008547 2 4 3 MPN, Breast chr12: 46765022-46765808 2 2 5 3 MPN, Prostate chr5: 157345785-157347510 2 4 3 Oral, Breast chr15: 32573790-32575001 2 1 4 3 Oral, Lymphoma chr2: 139375038-139376849 1 1 4 3 Breast, Oral chr1: 64080787-64082020 1 5 3 Lymphoma, Breast chr19: 32986379-32989682 1 4 3 Lymphoma, Gastric chr1: 238372430-238375019 1 2 1 4 3 Pancreas, Oral chr10: 21357922-21359678 1 1 4 3 Lymphoma, MPN chr14: 57677677-57678048 1 5 3 Breast, Lymphoma chr16: 4552399-4553233 3 11 3 Cervical, Lymphoma chrX: 36139141-36140020 6 3 Cervical, Gastric chr16: 51246583-51248855 2 7 3 Cervical, Lymphoma chr3: 97550893-97552589 1 4 3 Cervical, Lymphoma chr6: 151297464-151299652 1 4 3 Cervical, Lymphoma chrX: 62435062-62436548 5 3 Breast, Cervical chr7: 138506992-138509638 1 4 3 Lymphoma, Cervical chr2: 204206408-204208995 1 4 3 Lymphoma, Cervical chr15: 49024038-49025027 1 4 3 Lymphoma, Cervical chr7: 84495121-84497088 4 3 Lymphoma, Cervical chr17: 42855745-42858503 10 13 3 Breast, Prostate chr16: 17095569-17097803 5 3 Gastric, Cervical chr18: 22090016-22090564 2 6 3 Gastric, Prostate chr9: 37875565-37875969 1 10 3 Cervical, Colon chr11: 17030098-17030554 1 7 3 Colon, Kidney chr4: 68265004-68266433 1 4 3 Colon, Lymphoma chr1: 16890145-16890316 1 4 3 Colon, Kidney chr5: 108257676-108258248 3 5 3 Prostate, Colon chr4: 174790868-174792152 4 3 Lymphoma, Colon chr1: 87282633-87284966 4 3 Lymphoma, Cervical chr12: 40966857-40969856 5 3 Lymphoma, Cervical chr3: 187961542-187964137 7 3 Gastric, Cervical chr7: 16870050-16872687 3 9 3 Breast, Gastric chr11: 82597892-82598941 6 3 Gastric, Lymphoma chrX: 138942285-138943083 5 3 Gastric, Bladder chr8: 120561397-120562903 2 4 3 Prostate, Breast chr15: 100135383-100137014 1 5 3 Kidney, Lymphoma chr11: 16461350-16462832 4 3 Kidney, Breast chr11: 29253864-29254659 1 5 3 Lymphoma, Kidney chrX: 73296169-73299018 2 6 3 Lymphoma, Prostate chr2: 25932706-25933414 2 4 3 Prostate, Breast chr6: 143853283-143854931 1 9 3 Lymphoma, Kidney chr1: 42738096-42738591 7 3 Lymphoma, Breast chr13: 98665103-98666182 1 1 6 3 Lymphoma, MPN chr10: 13238600-13239995 1 6 3 Lymphoma, Breast chr1: 104417120-104419481 2 5 3 Lymphoma, Prostate chr14: 91136604-91139705 2 4 3 Prostate, Breast chr3: 73314742-73314982 4 3 Breast, Lymphoma chrX: 40578772-40580026 4 3 Lymphoma, Gastric chr4: 136186068-136187470 1 5 3 Lymphoma, Melanoma chr9: 5100700-5103470 9 17 3 MPN, Lymphoma chr18: 27796204-27798261 8 1 1 10 3 MPN, Oral chr14: 70866169-70867395 6 1 14 3 Lymphoma, MPN chr19: 21725455-21727418 6 15 3 Lymphoma, MPN chr1: 218865561-218868015 4 4 11 3 MPN, Prostate chr17: 55317138-55317916 4 3 8 3 MPN, Prostate chr7: 7986381-7988620 4 1 17 3 MPN, Lymphoma chr20: 31962213-31964566 3 6 3 MPN, Gastric chr2: 32280035-32282728 3 2 10 3 Lymphoma, MPN chr13: 21002739-21003960 3 6 3 MPN, Lymphoma chr7: 156680057-156683908 2 4 3 MPN, Bladder chr5: 67490784-67491620 2 4 3 MPN, Gastric chr10: 64650560-64652770 2 1 7 3 Lymphoma, MPN chr19: 23100389-23102504 2 4 3 MPN, Breast chr5: 72327995-72329739 2 2 10 3 Lymphoma, MPN chr13: 19542116-19543366 2 5 3 Lymphoma, MPN chr9: 107325071-107329784 2 5 3 Lymphoma, MPN chr10: 65061132-65064798 1 2 4 3 Prostate, Breast chrX: 72660041-72662733 1 2 4 3 Prostate, Lymphoma chr6: 139012261-139013805 1 1 4 3 Breast, MPN chr1: 40371010-40373921 1 4 8 3 Prostate, Breast chr10: 121370445-121373045 1 4 3 Lymphoma, Gastric chr20: 32452814-32454340 1 2 5 3 Lymphoma, Prostate chr12: 100881924-100882389 1 2 2 5 3 Pancreas, Prostate chr14: 81452361-81454170 1 5 3 Gastric, Lymphoma chr12: 70530011-70530466 1 5 3 Lymphoma, Kidney chr2: 231145010-231146919 2 1 6 3 Lymphoma, MPN chr7: 56602283-56604066 1 4 3 Cervical, Gastric chr5: 92628780-92629995 1 5 3 Colon, Lymphoma chr10: 66255316-66256651 1 4 7 3 Pancreas, Breast chr1: 16882259-16884855 1 2 4 3 Prostate, Breast chr15: 19186009-19190031 2 21 27 3 Breast, Prostate chr4: 129295826-129297562 1 14 18 3 Breast, Prostate chr17: 60204622-60205031 1 9 12 3 Prostate, Breast chr1: 201002645-201003292 1 7 10 3 Prostate, Breast chr8: 87563050-87564438 6 8 3 Prostate, Breast chr13: 18425000-18427904 1 4 3 Lymphoma, Bladder chr7: 63832277-63834664 1 5 3 Lymphoma, Breast chr15: 19270058-19270354 8 1 10 3 Prostate, Kidney chr7: 98435001-98435457 1 1 7 3 Lymphoma, MPN chr9: 96300008-96304864 2 1 5 3 Kidney, Prostate chr16: 21692-25029 1 10 4 Colon, Lymphoma chr21: 36588933-36589981 5 10 4 Prostate, Colon chr4: 68263271-68265012 1 5 4 Colon, Breast chr5: 108413260-108415011 5 13 4 Breast, Prostate chr7: 80128544-80129812 9 1 12 4 MPN, Gastric chrX: 149149690-149150027 5 1 9 4 MPN, Breast chr17: 71733295-71734754 5 2 10 4 MPN, Gastric chr5: 108147697-108149170 1 2 1 5 4 Oral, Breast chr4: 46420373-46421380 1 2 5 4 Oral, Breast chr17: 73665057-73666771 2 5 4 Oral, Cervical chr7: 104957816-104958449 1 6 4 Breast, Gastric chr11: 122335815-122337882 4 7 4 Prostate, Bladder chr22: 23903543-23904988 4 9 25 4 Prostate, Pancreas chr17: 22433702-22435031 1 1 6 4 Breast, Lymphoma chrX: 114805474-114806874 7 4 Cervical, Gastric chr17: 26359119-26359614 2 8 4 Lymphoma, Cervical chr15: 7919666 1 6 4 Cervical, Lymphoma chr13: 28070998-28072283 5 4 Cervical, Gastric chr6: 31351298-31355026 2 7 4 Lymphoma, Prostate chrX: 70176246-70179958 1 2 5 4 Prostate, Cervical chr3: 25771373-25774090 1 1 6 4 Lymphoma, Cervical chr19: 14042134-14043294 1 2 11 4 Breast, Prostate chrX: 49283282-49284875 1 6 4 Gastric, Cervical chr22: 39511857-39515009 1 10 4 Colon, Lymphoma chr6: 138067402-138069986 1 6 4 Colon, Cervical chr3: 197148302-197149669 1 8 4 Colon, Kidney chr17: 72157677-72159762 15 4 Gastric, Lymphoma chr5: 95130415-95132592 1 9 4 Cervical, Colon chr2: 91318683-91319881 5 4 Colon, Cervical chr6: 30707737-30709987 1 6 4 Colon, Lymphoma chrX: 135716676-135717846 5 9 4 Prostate, Colon chr17: 25951505-25952090 2 6 4 Colon, MPN chr6: 30107367-30109699 2 1 6 4 Colon, MPN chr16: 16366198-16368408 6 4 Gastric, Kidney chr13: 76460074-76462820 1 9 4 Lymphoma, Bladder chr22: 40726971-40728762 1 2 5 4 Prostate, Colon chr3: 123862123-123865031 1 1 5 4 Lymphoma, Colon chr6: 128942962-128943901 1 5 4 Breast, Colon chr2: 202908139-202909954 1 6 4 Lymphoma, Cervical chr13: 88810056-88813657 7 4 Lymphoma, Breast chr13: 36410025-36411827 7 4 Gastric, Colon chrX: 120164368-120165004 1 7 4 Gastric, Lymphoma chrX: 70451371-70452584 3 8 4 Prostate, Gastric chr7: 98432519-98435031 4 14 4 Lymphoma, Prostate chr1: 78085216-78088009 22 32 4 Lymphoma, Kidney chr1: 152090703-152092464 1 5 4 Kidney, Breast chr7: 137395348-137395688 1 1 5 4 Kidney, Melanoma chr11: 66285096-66286445 10 15 4 Breast, Kidney chr7: 127889632-127889961 1 5 4 Kidney, Cervical chr1: 241495850-241498178 1 1 9 4 Lymphoma, Kidney chr12: 74606217-74606813 1 3 6 4 Prostate, Gastric chr12: 78225570-78226943 4 7 4 Prostate, Breast chr1: 169906030-169906835 1 1 9 4 Lymphoma, Breast chr2: 224277513-224278767 9 4 Melanoma, Gastric chr12: 64912853-64915025 9 1 13 4 MPN, Lymphoma chr19: 59425000-59426807 8 11 4 MPN, Cervical chr6: 36167532-36168612 8 1 18 4 MPN, Lymphoma chr9: 70415029-70417781 7 13 4 MPN, Lymphoma chr15: 63850100-63851589 6 4 19 4 Lymphoma, MPN chr1: 203861013-203862993 6 20 28 4 MPN, Prostate chr6: 111285905-111288987 6 1 1 13 4 MPN, Lymphoma chr6: 36750047-36751612 6 1 9 4 MPN, Cervical chr3: 133590336-133594125 5 7 14 4 Prostate, MPN chr5: 172445309-172447866 5 2 1 12 4 MPN, Lymphoma chr7: 79844651-79844976 5 1 9 4 MPN, Cervical chr3: 76565834-76568498 3 6 4 MPN, Cervical chr12: 70528835-70530029 3 4 16 4 Lymphoma, Prostate chr14: 69770604-69771489 2 2 6 4 MPN, Prostate chrX: 18269212-18269601 2 5 4 MPN, Breast chr3: 23895319-23895949 2 10 4 Lymphoma, MPN chr3: 155553099-155554758 1 6 4 Gastric, Lymphoma chr2: 48712985-48713883 1 5 4 Lymphoma, Gastric chr17: 78125786-78128688 1 8 13 4 Prostate, Breast chr8: 124318219-124318608 3 2 1 9 4 Breast, MPN chr14: 63130269-63131835 2 2 13 4 Lymphoma, Colon chr9: 89871235-89875006 1 1 6 4 Kidney, Lymphoma chrX: 63570009-63572264 1 2 5 4 Prostate, Cervical chr1: 245420253-245420689 3 1 1 8 4 Lymphoma, MPN chr5: 21918407-21920011 1 6 4 Colon, Gastric chr5: 31959147-31959652 4 1 1 7 4 MPN, Lymphoma chr1: 164511305-164513491 4 1 1 8 4 MPN, Lymphoma chr4: 66642565-66643009 5 1 1 8 4 MPN, Breast chr9: 33009522-33010029 1 2 5 4 Prostate, Breast chr17: 10560021-10560742 2 18 23 4 Kidney, MPN chrX: 41420046-41420852 1 10 4 Lymphoma, Breast chr2: 135985004-135986146 1 8 5 Colon, Lymphoma chr16: 31486617-31488548 1 2 1 8 5 Gastric, Oral chr12: 17034921-17035029 1 1 1 6 5 Lymphoma, Gastric chr7: 143975043-143976509 1 7 5 Gastric, Lymphoma chr7: 88106317-88107757 1 2 7 5 Lymphoma, Breast chr10: 21952707-21955029 2 2 15 5 Cervical, Lymphoma chr7: 117310724-117311343 2 18 5 Cervical, Colon chr2: 41900352-41902242 1 9 5 Cervical, Breast chr4: 4946239-4947833 9 5 Cervical, Lymphoma chr5: 114752657-114755023 11 5 Gastric, Cervical chr4: 146516051-146518502 3 2 12 5 Cervical, Gastric chr3: 174029034-174029700 6 5 Cervical, Bladder chr4: 358246-359943 1 1 7 5 Cervical, Lymphoma chr5: 107088630-107089995 1 3 13 5 Lymphoma, Prostate chr4: 131043706-131044827 7 5 Cervical, Lymphoma chr13: 28191258-28194994 8 5 Cervical, Gastric chr2: 179027517-179028802 1 6 5 Lymphoma, Cervical chr15: 91140001-91141446 1 8 19 5 Prostate, Cervical chr16: 46156547-46158361 2 1 9 5 Colon, Lymphoma chr3: 39375064-39376459 2 3 14 5 Lymphoma, Colon chr19: 1153449-1154923 3 1 11 5 Cervical, Colon chr4: 110693368-110694731 1 1 6 5 Colon, Cervical chrX: 115981067-115982444 6 5 Colon, Cervical chr5: 37245024-37248385 1 12 5 Lymphoma, Colon chr4: 79320311-79322415 1 8 5 Lymphoma, Colon chr22: 22600024-22604137 3 4 12 5 Prostate, MPN chr5: 177330758-177333479 1 3 27 35 5 Pancreas, Prostate chr8: 82692562-82693415 2 3 8 5 Prostate, Pancreas chrY: 11781394-11785025 1 4 10 5 Prostate, Lymphoma chrX: 73266994-73269840 1 4 9 5 Prostate, Lymphoma chr16: 15137027-15139197 1 3 7 5 Prostate, Breast chr12: 1843255-1844894 1 1 8 5 Gastric, Cervical chr11: 119196989-119198204 9 35 5 Prostate, Kidney chr6: 25131126-25132842 3 1 18 5 Kidney, Lymphoma chr2: 152954216-152955031 1 1 9 5 Kidney, Breast chr2: 25898653-25900030 3 4 20 5 Lymphoma, Kidney chr3: 97977193-97979955 1 1 10 5 Lymphoma, Gastric chr3: 52382585-52384174 8 1 18 5 MPN, Lymphoma chr1: 245420126-245420978 8 1 20 5 MPN, Lymphoma chrX: 73719066-73719697 6 1 17 5 MPN, Lymphoma chr1: 212722108-212723497 6 13 5 MPN, Cervical chr11: 92908039-92909143 5 2 1 13 5 MPN, Lymphoma chr21: 44290157-44291481 5 17 5 Lymphoma, MPN chr1: 158906538-158909903 5 17 5 Lymphoma, MPN chr12: 3820029-3825029 4 1 12 5 Lymphoma, MPN chr14: 54835005-54835966 4 18 31 5 Lymphoma, MPN chr15: 91077671-91078734 4 16 1 23 5 MPN, Prostate chr6: 147770007-147774161 4 4 1 13 5 MPN, Prostate chr8: 75677664-75679288 2 1 6 5 MPN, Breast chr6: 57002238-57004469 2 1 6 5 MPN, Gastric chr19: 3821749-3823145 2 10 5 Gastric, Lymphoma chr1: 245410530-245415024 2 1 8 5 Kidney, Lymphoma chr17: 63602780-63604389 2 1 1 7 5 Cervical, Oral chr5: 60223151-60223641 1 2 8 5 Colon, Lymphoma chr17: 18515359-18517127 2 1 7 5 Colon, Oral chr11: 129407907-129408375 5 2 2 11 5 MPN, Oral chr5: 68645003-68645660 2 2 11 20 5 Colon, Lymphoma, chr5: 43530817-43532401 1 1 8 5 Lymphoma, Breast chr5: 14850010-14851722 1 1 5 9 5 Prostate, Cervical chr9: 130067782-130069317 1 3 7 5 Prostate, Cervical chr9: 21685064-21689997 1 1 7 5 Gastric, Bladder chr1: 226368927-226369874 1 7 5 Cervical, Lymphoma chr13: 78381046-78382898 1 1 1 6 5 Cervical, Melanoma chrX: 75471475-75472671 1 8 5 Lymphoma, Cervical chr2: 236455494-236455892 3 1 2 9 5 MPN, Gastric chr10: 76705756-76706390 1 18 5 Lymphoma, Gastric chr10: 79160515-79164753 10 4 19 5 Cervical, Colon chr1: 97785042-97785538 1 1 2 6 5 Cervical, Gastric chr7: 6647990-6650019 1 1 2 13 5 Lymphoma, Gastric chr13: 18423767-18425026 2 1 7 5 Lymphoma, Prostate chr19: 9746149-9746855 1 2 1 6 5 Prostate, Cervical chr17: 20628146-20629946 2 3 2 19 6 Breast, Pancreas chr1: 76938038-76939270 1 1 1 9 6 Breast, Gastric chr2: 162065731-162069847 1 1 7 6 Gastric, Breast chr1: 245429261-245429363 1 2 4 15 6 Lymphoma, Breast chr22: 21935039-21937130 1 6 2 14 6 Prostate, Lymphoma chr19: 15881767-15883707 4 12 23 6 Pancreas, Bladder chr2: 158630084-158632092 2 1 12 6 Cervical, MPN chr17: 24552608-24554860 1 14 6 Cervical, Colon chr7: 158107538-158109026 1 14 6 Cervical, Colon chr15: 88619130-88620026 7 20 50 6 Pancreas, Cervical chr18: 55835065-55835698 1 3 2 14 6 Cervical, Lymphoma chr2: 84856616-84858887 1 13 6 Lymphoma, Cervical chr8: 62011957-62014951 1 4 16 6 Lymphoma, Prostate chr9: 6656022-6660031 1 3 19 6 Lymphoma, Kidney chr2: 91130114-91132611 1 2 10 6 Gastric, Cervical chr9: 6660006-6664836 3 17 6 Lymphoma, Prostate chr11: 232267-233719 6 1 2 27 6 Lymphoma, Colon chr12: 74737397-74739842 8 11 48 6 MPN, Cervical chr6: 127717472-127720031 3 15 6 Colon, Kidney chr16: 25046-28284 1 1 12 6 Colon, Lymphoma chr8: 55046759-55049918 6 4 27 6 MPN, Colon chr7: 56261370-56264649 4 1 14 6 Lymphoma, MPN chr15: 73400772-73402108 4 1 22 6 Lymphoma, Gastric chr5: 175667341-175669888 2 1 1 15 6 Lymphoma, Colon chr21: 36345013-36346248 2 2 10 6 Colon, Lymphoma chr2: 222535085-222537390 1 9 6 Colon, Gastric chr7: 5566916-5567375 1 1 9 6 Breast, Bladder chrX: 130608331-130609932 4 11 6 Prostate, Breast chrX: 113915399-113917620 22 6 Gastric, Lymphoma chr13: 27686701-27688179 2 1 12 6 Lymphoma, Kidney chr8: 59500000-59502148 7 1 22 6 Lymphoma, MPN chr17: 27578894-27579439 6 1 3 3 21 6 Lymphoma, MPN chr7: 30528821-30529744 6 3 2 21 6 Lymphoma, MPN chr11: 91708751-91709133 6 1 3 4 17 6 MPN, Prostate chr17: 20456347-20460008 5 1 1 15 6 Lymphoma, MPN chr11: 133498167-133500014 5 15 6 MPN, Gastric chr1: 207507608-207508364 5 1 1 1 14 6 Lymphoma, MPN chr16: 18386391-18389697 5 3 1 15 6 MPN, Lymphoma chr17: 27461314-27463910 4 2 3 15 6 Lymphoma, MPN chr10: 59642034-59642720 4 1 13 6 Lymphoma, MPN chr10: 94417431-94419676 4 1 15 6 Lymphoma, MPN chrX: 48519005-48520014 4 4 1 17 6 Lymphoma, MPN chr9: 126952546-126954985 3 13 28 6 Breast, Lymphoma chr9: 34308269-34310028 2 9 6 Breast, Colon chr13: 48243346-48243963 4 2 1 17 6 Lymphoma, MPN chrX: 85225950-85227916 1 3 2 12 6 Breast, Pancreas chr14: 95758990-95760012 1 2 1 12 6 Gastric, Cervical chr4: 145986182-145988340 1 1 11 6 Gastric, Lymphoma chr7: 22516700-22518121 3 1 1 9 6 MPN, Lymphoma chr10: 43420007-43421764 3 1 1 9 6 MPN, Gastric chr17: 63634210-63634432 1 1 1 8 6 Breast, Colon chr12: 48067082-48070015 1 1 12 6 Lymphoma, Colon chr9: 138826841-138829981 1 1 2 9 6 Cervical, Colon chr10: 79210011-79211784 1 1 1 7 6 Colon, Cervical chr6: 109335327-109335840 1 2 11 6 Lymphoma, Colon chr1: 229223694-229225016 3 1 1 10 6 MPN, Colon chr15: 34692846-34694996 4 1 10 6 MPN, Gastric chrX: 67920024-67922986 1 1 11 6 Lymphoma, Cervical chrX: 51683397-51683809 5 1 1 4 15 6 MPN, Prostate chr6: 131545798-131548372 3 13 6 Lymphoma, Cervical chr10: 135007719-135008625 1 8 6 Gastric, Lymphoma chr10: 127345241-127346621 2 1 15 7 Breast, Melanoma chr22: 19134094-19135031 1 2 14 27 7 Lymphoma, Kidney chr15: 43132056-43133113 2 2 5 14 7 Prostate, Gastric chr2: 106680143-106681581 2 2 12 7 Lymphoma, MPN chr12: 119766955-119768000 1 1 5 18 7 Breast, Prostate chr6: 53207834-53209186 1 1 31 7 Cervical, Lymphoma chr9: 30678968-30680030 1 1 16 7 Cervical, Colon chr17: 64826385-64826952 2 1 1 25 7 Cervical, Colon chr7: 150830163-150832517 7 1 2 29 7 Lymphoma, MPN chr21: 38796179-38796358 1 20 7 Gastric, Colon chr1: 16885318-16888034 1 1 21 7 Breast, Colon chr12: 99496386-99499915 5 1 21 7 Colon, MPN chr13: 44861259-44863071 1 9 1 20 7 Prostate, Colon chr9: 124488119-124489981 1 1 3 23 7 Gastric, Prostate chrX: 65210128-65212872 1 2 13 7 Lymphoma, Colon chr15: 91139708-91140030 4 1 15 7 Prostate, Melanoma chr1: 166055742-166056259 1 10 26 7 Gastric, Breast chr9: 16765715-16765767 1 1 2 11 7 Gastric, Breast chr2: 171165069-171166985 10 7 Gastric, Bladder chr3: 157187740-157189549 3 1 30 7 Lymphoma, Colon chr12: 19985423-19989724 1 4 17 7 Gastric, Prostate chr9: 98527969-98529661 1 4 13 7 Prostate, Lymphoma chr7: 46005000-46007016 1 3 10 7 Prostate, Lymphoma chr2: 85421131-85422577 1 1 4 18 7 Breast, Prostate chr12: 86700634-86702602 2 12 7 Lymphoma, Melanoma chr15: 97615266-97617895 1 1 2 9 7 Gastric, Prostate chr13: 40090629-40094438 8 3 1 26 7 MPN, Lymphoma chr17: 30756783-30758835 7 2 4 18 7 MPN, Prostate chr17: 4072185-4075029 6 10 28 7 Lymphoma, MPN chr19: 45140233-45141668 5 2 16 7 Lymphoma, MPN chr17: 30850001-30851322 5 2 24 7 Lymphoma, MPN chr2: 202772424-202775011 2 1 8 7 MPN, Breast chr12: 109351042-109353797 1 2 2 10 7 Colon, Oral chr10: 75161319-75163908 3 2 5 30 50 7 Breast, Pancreas chr21: 46897231-46898445 4 2 2 18 7 Lymphoma, MPN chr15: 54085179-54086686 2 4 17 7 Cervical, Pancreas chr5: 25945144-25949126 7 2 1 1 17 7 MPN, Cervical chr3: 185226809-185228146 1 1 1 12 7 Lymphoma, Breast chr7: 20588278-20589374 2 1 1 10 7 Lymphoma, MPN chr3: 44595235-44597668 1 9 1 15 7 Prostate, Breast chr7: 39575135-39576400 1 4 6 26 7 Lymphoma, Prostate chr1: 51395688-51396740 3 1 1 1 12 7 Breast, MPN chr14: 64815693-64817730 1 5 1 17 7 Lymphoma, Pancreas chr1: 16006265-16007067 2 1 2 1 13 7 Kidney, Lymphoma, chr5: 177525251-177526202 1 2 1 15 7 Breast, Melanoma chr1: 144990000-144992583 3 1 13 7 Gastric, MPN chr7: 55672416-55674246 4 1 1 13 7 Gastric, MPN chr5: 114875647-114877498 1 1 1 9 7 Cervical, Breast chr2: 101256951-101257613 5 1 2 22 7 Lymphoma, MPN chr7: 27462505-27465027 5 1 1 11 7 MPN, Cervical chrX: 100676203-100679915 3 11 2 23 7 Kidney, MPN chr3: 171262714-171264755 1 2 1 10 7 Gastric, Prostate chr3: 52202197-52204001 2 2 2 2 22 8 Lymphoma, MPN chrX: 25573624-25574445 2 2 34 8 Lymphoma, Cervical chr2: 191565081-191567610 8 4 1 31 8 MPN, Cervical chrX: 53210000-53210656 5 4 36 8 Cervical, Colon chrX: 41417881-41420027 4 23 8 Cervical, Lymphoma, chr5: 43622114-43624741 1 6 28 8 Prostate, Cervical chr1: 218493241-218494999 5 1 1 26 8 Lymphoma, Gastric chr3: 95276627-95278752 9 4 46 8 MPN, Cervical chr6: 160051470-160055015 1 10 2 41 8 Lymphoma, Colon chr12: 55190981-55193352 2 1 28 8 Lymphoma, Colon chr3: 48272166-48273216 6 1 14 41 8 MPN, Colon chr11: 6465021-6467394 7 1 3 33 8 MPN, Colon chrX: 81638952-81640007 1 1 2 27 8 Gastric, Cervical chr4: 118715123-118716642 5 1 2 27 8 Cervical, Colon chr12: 110590068-110592654 5 2 26 8 Lymphoma, MPN chr20: 48963622-48964977 4 1 5 29 8 Prostate, Colon chr4: 22337134-22338823 7 24 8 MPN, Lymphoma chr11: 61895019-61899450 4 15 34 8 Kidney, MPN chr1: 52606731-52607671 1 6 20 1 41 8 Pancreas, Breast chr19: 58005048-58009278 11 28 8 Lymphoma, Gastric chr4: 88053138-88055031 2 11 2 38 8 Lymphoma, Colon chr17: 30848980-30850029 6 3 1 36 8 Kidney, MPN chr6: 30262288-30264297 8 1 5 33 8 MPN, Prostate chr9: 119885003-119885562 6 1 2 2 20 8 MPN, Lymphoma chr12: 54660003-54663591 5 6 1 23 8 Lymphoma, Prostate chr10: 70062143-70062538 2 3 15 8 Gastric, Prostate chr12: 19500335-19502091 2 3 17 8 Gastric, Lymphoma chr17: 39660007-39663513 3 2 2 2 1 16 8 Breast, MPN chr12: 16442198-16445014 1 2 1 11 8 Cervical, Colon chrX: 120165030-120166529 2 1 15 8 Lymphoma, Breast chr15: 51016593-51017949 4 2 3 30 8 Gastric, Lymphoma chr22: 40833082-40834984 6 2 1 6 24 8 MPN, Prostate chr12: 3818860-3819919 6 2 1 30 8 MPN, Cervical chr2: 74498320-74499480 2 1 19 8 Lymphoma, Colon chr2: 138761156-138762932 4 2 1 2 27 8 Lymphoma, Colon chr8: 30215043-30218410 1 1 1 1 13 8 Lymphoma, Gastric chr13: 64430032-64431456 1 1 1 13 8 Gastric, Breast chr1: 96685035-96686396 1 1 1 11 8 Lymphoma, Gastric chr10: 32840157-32840929 1 1 3 15 8 Lymphoma, Prostate chrX: 65092271-65093777 4 1 1 15 8 MPN, Cervical chr17: 2436284-2437919 1 1 12 8 Cervical, Lymphoma chr2: 127030021-127032314 2 1 14 8 Cervical, Gastric chr15: 19190000-19191609 2 1 36 49 8 Breast, Prostate chr9: 22001477-22002779 5 1 23 8 Lymphoma, MPN chr1: 177437318-177437893 1 2 20 8 Gastric, Lymphoma, chr4: 98042943-98043372 8 1 1 4 30 9 MPN, Cervical chr10: 107436038-107439382 2 1 1 26 9 Cervical, Colon chr3: 15895007-15896926 1 1 1 15 9 Cervical, Colon chr7: 144911241-144912979 1 4 1 23 9 Cervical, Gastric chrX: 44377591-44379921 2 1 2 30 9 Lymphoma, Colon chrX: 73340516-73344880 7 1 21 60 9 MPN, Colon chr12: 67322298-67323260 9 1 5 46 9 MPN, Cervical chr7: 72033364-72034127 2 2 2 23 9 Colon, Gastric chr1: 89067086-89067800 9 2 7 54 9 MPN, Prostate chrX: 135755159-135758921 1 17 1 47 9 Lymphoma, Colon chr5: 68644250-68645023 1 1 6 22 9 Prostate, Colon chr21: 31920001-31923002 1 4 27 9 Lymphoma, Kidney chr22: 24373154-24375027 7 28 65 9 Kidney, MPN chr22: 22320853-22325031 2 7 2 28 9 Kidney, Prostate chr3: 53070978-53074165 2 1 2 1 23 9 Lymphoma, Kidney chr1: 89341252-89343268 9 14 2 56 9 MPN, Kidney chr6: 86193656-86194482 7 1 2 30 9 Lymphoma, MPN chr4: 39650588-39652334 4 2 20 9 Lymphoma, MPN chr3: 139081781-139083983 1 2 1 1 17 9 Lymphoma, Breast chrX: 65635098-65636615 1 2 3 1 14 9 Cervical, Pancreas chr7: 10457157-10459773 2 2 31 9 Breast, Gastric chr7: 151694812-151694991 1 2 1 2 27 9 Lymphoma, Breast chr12: 4076871-4079190 2 2 1 1 22 9 Lymphoma, Colon chrX: 13306389-13307499 6 2 2 22 9 MPN, Colon chr14: 61368169-61368862 7 2 7 7 42 9 Breast, MPN chr10: 23465825-23468573 4 2 2 29 9 Cervical, Gastric chr3: 182442769-182443381 8 2 6 5 41 9 MPN, Lymphoma chr8: 107777994-107779579 9 2 1 25 9 MPN, Lymphoma chr1: 72512203-72513454 9 2 3 27 9 MPN, Lymphoma chr14: 35420023-35420673 2 1 27 9 Lymphoma, Cervical chrX: 79711705-79715004 4 1 1 1 17 9 Lymphoma, MPN chr1: 245460000-245461944 1 1 1 19 9 Lymphoma, Cervical chr3: 27649231-27650012 1 3 7 32 9 Prostate, Kidney chr16: 14920001-14923862 2 7 1 21 9 Prostate, Gastric chr6: 158950293-158952897 7 2 1 7 55 10 Cervical, MPN chrX: 70555627-70557712 8 2 1 20 4 71 10 MPN, Cervical chr7: 32762364-32763505 5 1 7 3 52 10 Cervical, Lymphoma chr19: 35220001-35221268 4 13 1 52 10 Kidney, Lymphoma chr3: 122007401-122009653 5 1 6 3 46 10 Cervical, Prostate chr3: 40612582-40613978 2 2 7 2 46 10 Lymphoma, Prostate chr12: 41110881-41113477 5 2 4 43 10 Cervical, Colon chr1: 233967900-233969581 9 2 3 42 10 MPN, Cervical chr9: 32935789-32937584 5 1 4 2 40 10 Colon, MPN chr1: 106235172-106236952 8 7 4 49 10 MPN, Pancreas chr20: 60947228-60948154 2 2 3 1 37 10 Cervical, Colon chr12: 51833223-51834834 5 2 1 1 36 10 Lymphoma, Gastric chr12: 13046376-13049181 7 1 6 35 10 MPN, Prostate chr19: 14461030-14461871 1 2 8 2 34 10 Prostate, Cervical chr7: 65525025-65526430 3 6 34 10 Lymphoma, Prostate chr9: 88816231-88818084 1 1 14 3 32 10 Cervical, Colon chr3: 115086410-115088196 1 1 1 1 30 10 Kidney, Lymphoma chr8: 48585762-48587345 6 1 2 29 10 Lymphoma, MPN chr1: 240223113-240224419 4 2 1 23 10 Lymphoma, MPN chr3: 36783146-36785030 1 1 13 10 Colon, Gastric chr1: 145141125-145143358 9 2 1 24 89 11 MPN, Breast chr10: 71593210-71594625 8 2 6 24 85 11 Cervical, Gastric chr7: 137738291-137739988 9 2 4 4 75 11 MPN, Cervical chr22: 24375001-24378128 8 1 8 12 74 11 Breast, Lymphoma chr9: 97948095-97950029 7 2 9 2 73 11 Prostate, Cervical chrX: 115766164-115766603 8 3 16 70 11 Lymphoma, MPN chr7: 104095351-104099270 8 5 2 58 11 Gastric, Cervical chr12: 12155020-12156368 6 2 2 57 11 Cervical, Colon chrX: 74880003-74883639 2 5 30 1 81 11 Gastric, Cervical chr2: 61016549-61018625 9 2 4 1 53 11 MPN, Cervical chr6: 143705076-143706473 2 1 8 2 53 11 Kidney, Prostate chr3: 48306896-48308964 5 1 14 3 61 11 Kidney, Colon chr17: 37935489-37939966 9 3 1 52 11 Gastric, Lymphoma chr5: 96416174-96418578 7 2 3 1 59 11 Cervical, MPN chr22: 29627969-29630029 7 12 3 59 11 MPN, Cervical chr1: 116875720-116878445 9 2 3 2 48 11 MPN, Breast chr10: 120681594-120682842 1 2 1 4 43 11 Lymphoma, Cervical chr11: 18465871-18469227 5 1 7 43 11 Prostate, MPN chr9: 12962422-12963578 8 2 1 6 42 11 Cervical, MPN chr9: 34911199-34912896 6 2 3 49 11 Cervical, Lymphoma chr17: 11959531-11959908 2 2 5 10 2 49 11 Colon, Pancreas chr19: 18002173-18005024 3 1 2 1 36 11 Lymphoma, Colon chr20: 17940242-17942547 4 1 4 1 36 11 Cervical, Gastric chr4: 74183155-74184968 1 2 1 7 3 35 11 Lymphoma, Prostate chr6: 144563059-144563906 6 2 1 5 2 39 11 Gastric, MPN chr7: 124460752-124462651 4 1 1 6 38 11 Prostate, Breast chr9: 14910713-14912555 2 2 1 1 28 11 Lymphoma, Cervical chr22: 30995341-30999218 1 1 2 50 1 71 11 Prostate, Breast chr22: 24075369-24076698 3 1 1 3 1 26 11 Lymphoma, Colon chrY: 11770408-11775026 1 2 23 73 3 180 12 Kidney, Prostate chr11: 43875453-43878110 8 2 8 32 3 109 12 Gastric, MPN chrX: 23003631-23004877 1 18 13 4 81 12 Bladder, Lymphoma chr12: 32770077-32771796 9 2 20 3 87 12 Kidney, MPN chr1: 75980428-75983188 7 1 1 14 2 68 12 MPN, Breast chr6: 74058239-74059970 2 2 2 19 66 12 Gastric, Kidney chr18: 1350751-1353998 1 2 8 9 1 60 12 Prostate, Pancreas chr17: 25420266-25421375 4 1 7 16 1 59 12 Breast, Pancreas chrX: 114843363-114844764 4 2 1 6 2 52 12 Kidney, Prostate chr16: 11905084-11905547 1 5 4 1 47 12 Pancreas, Colon chr4: 10982554-10984464 6 2 1 12 1 55 12 Lymphoma, MPN chrX: 30558147-30559009 7 2 4 2 45 12 Gastric, Lymphoma chr12: 9283162-9284461 8 2 1 1 53 12 Cervical, MPN chr16: 68346815-68349469 2 2 4 1 40 12 Lymphoma, Cervical chr6: 5917621-5919864 2 2 9 2 1 40 12 Pancreas, Breast chr5: 75708184-75708770 6 2 24 62 4 229 13 Bladder, Cervical chrX: 74875425-74880031 9 2 10 71 4 190 13 MPN, Prostate chr17: 60176781-60178361 9 2 14 67 4 194 13 MPN, Prostate chr11: 113145499-113147696 6 2 15 47 1 163 13 Cervical, Kidney chr2: 234438687-234440030 3 2 15 47 2 139 13 Lymphoma, Cervical chr17: 63636429-63636974 5 2 21 60 3 197 13 Prostate, Colon chr3: 117845959-117848342 8 2 17 23 1 143 13 MPN, Cervical chrX: 122077782-122079346 4 2 5 23 4 125 13 Kidney, Cervical chr2: 234440001-234441782 3 2 13 33 1 120 13 Lymphoma, Cervical chr11: 33051914-33054815 9 2 2 23 4 108 13 MPN, Cervical chr10: 42335001-42336262 9 2 1 27 3 107 13 Kidney, MPN chr18: 12056629-12058570 5 1 12 25 2 107 13 Kidney, MPN chr3: 180460196-180461897 7 2 4 36 3 102 13 Gastric, MPN chr22: 19135000-19137681 3 2 1 37 3 99 13 Kidney, Cervical chr17: 60380103-60384663 6 2 1 18 4 77 13 Kidney, Cervical chr20: 3952190-3953301 9 2 2 7 1 76 13 Lymphoma, MPN chr12: 6864001-6865025 7 2 2 10 3 79 13 Kidney, MPN chr12: 62501627-62504537 4 2 2 17 1 61 13 Breast, Lymphoma chr2: 132196980-132198589 5 2 2 6 2 60 13 Gastric, Breast chr1: 114880845-114882611 2 2 4 3 1 60 13 Kidney, Cervical

TABLE 4 CANCER BENIGN Pan- Pros- Lympho- Pan- Pros- Ψ-Chromosomal Breast Gastric CLL creas tate Breast Gastric blast creas tate Region Ψ-Name ENCODE Yale (53) (21) (11) (25) (71) (18) (4) (8) (3) (18) chr10: 37577033-37577556 ATP8A2 manual dup 8 chr10: 37636369-37640031 ATP8A2 manual 6 chr10: 37590732-37594328 ATP8A2 manual dup 6 chr10: 37640002-37644728 ATP8A2 manual 5 chr4: 141781899-141782720 KIAA1856 dup 4 chr10: 37666189-37668498 TMEM161B manual proc 4 chr18: 70208031-70208617 FAU proc 3 chr19: 12531356-12532856 PGK1 manual dup 3 chr22: 23438167-23438592 CRIP1 manual proc 3 chr9: 75280000-75280934 DPP3 manual proc 3 chr12: 110503660-110503886 IFITM1 proc 5 chr13: 36410025-36411827 EIF4A1 manual proc 4 chrX: 138942285-138943083 HNRNPA3 manual proc 3 chr19: 21725455-21727418 CCNYL1 proc 8 chr21: 44290157-44291481 H2AFZ manual dup 8 chr6: 143853283-143854931 VDAC1 manual proc 7 chr13: 40464767-40464951 RGS17 manual proc 6 chrX: 46468751-46470028 CHMP5 manual proc 6 chr1: 202041181-202041985 CHMP5 manual proc 6 chr2: 201982582-201984995 SCYL2 manual proc 6 chr6: 139701047-139702459 DNAJC7 manual proc 5 chr7: 98435001-98435457 RNF14 manual proc 5 chr3: 115431891-115434722 KIAA1539 proc 4 chr2: 106680143-106681581 EEF1A1 manual dup 4 chr2: 201985004-201986130 SCYL2 manual proc 4 chrX: 110747689-110749928 EIF4B manual proc 4 chr10: 75852293-75853672 RAB5C manual proc 4 chr6: 90581057-90582594 FAM64A manual proc 4 chr13: 40465037-40465571 RGS17 manual proc 4 chr15: 81278450-81278844 BC117556 auto 3 chr4: 135468269-135469814 PES1 proc 3 chr12: 70530011-70530466 MRS2 proc 3 chr4: 103870768-103875031 MANBAL proc 3 chr10: 31689689-31689904 SPTLC1 manual frag 3 chr7: 23625349-23630025 FCF1 manual dup 3 chr12: 40966857-40969856 IGF2BP2 auto proc 3 chr1: 202765009-202765499 PEF1 manual proc 3 chr10: 75957261-75958035 MRPL35 manual proc 3 chr15: 19267708-19269952 CXADR auto proc 9 chr15: 19270058-19270354 CXADR auto proc 8 chrX: 135716676-135717846 RAN manual proc 5 chr11: 18573250-18574450 MTCH1 proc 4 chr10: 104925212-104926869 MARCKSL1 manual proc 4 chr3: 198845497-198847337 PPP4R2 dup 3 chr2: 132075527-132076801 AY458019 manual 3 chr17: 55317138-55317916 NDUFB8 proc 3 chr6: 1458119-1459994 ELF2 manual proc 3 chr21: 32790823-32791600 EXOSC3 manual proc 3 chr5: 110312099-110314335 BCLAF1 dup 1 2 chr4: 119333317-119335028 FKBP4 proc 1 2 chr15: 34696499-34699553 LARP4 proc 1 2 chr2: 25932706-25933414 ENO3 manual frag 1 2 chr10: 65061132-65064798 MRPL35 manual proc 1 2 chr6: 139012261-139013805 MTCH1 manual frag 2 1 chr16: 15137027-15139197 PKD1 manual dup 1 3 chr17: 18510983-18512998 FOXO3 manual 1 2 chr8: 124318219-124318608 UBA52 proc 3 1 chr1: 177822435-177824942 CENTG2 manual proc 3 1 chr5: 25945144-25949126 MSN proc 1 1 1 chr7: 75540406-75544538 LOC285908 manual proc 1 4 chr3: 73060699-73061349 FTH1 proc 1 2 chr14: 69770604-69771489 FLJ00248 proc 1 2 chr11: 129407907-129408375 TCEB2 proc 1 2 chr2: 132196348-132197314 BC016035 manual proc 1 2 chr2: 139375038-139376849 AHCY manual proc 2 1 chr12: 16442198-16445014 SUPT16H proc 1 1 1 chr2: 158630084-158632092 PTP4A1 manual proc 1 1 1 chr1: 16882259-16884855 EIF1AX manual 1 1 2 chr5: 108257676-108258248 LSM2 proc 1 3 chr17: 63634210-63634432 DQ587552 dup 2 1 1 chr8: 120561397-120562903 ZNF532 auto frag 1 1 2 chr12: 100881924-100882389 NENF proc 2 2 chr1: 145020394-145021949 SSB manual proc 2 1 chr10: 43420007-43421764 CAP1 manual proc 2 1 chr1: 40371010-40373921 OAZ1 manual proc 3 4 chr14: 60316280-60317538 MAD2L1 proc 1 2 chr3: 31470003-31472686 THRAP3 manual dup 1 2 chrX: 70176246-70179958 SOCS5 manual dup 1 2 chrX: 70180396-70182077 SOCS5 manual dup 1 2 chr9: 83890554-83893228 DDX10 manual proc 1 2 chrX: 72660041-72662733 MAP2K4 manual proc 1 2 chr8: 75677664-75679288 PCBP2 proc 1 1 1 chr4: 68263271-68265012 ST3GAL1 auto proc 1 1 1 chr3: 73314742-73314982 CCDC75 auto proc 2 1 chr13: 29768191-29769131 PRDX2 manual proc 2 1 chr12: 74606217-74606813 TMEM141 proc 1 1 3 chr6: 127717472-127720031 YWHAZ manual dup 1 3 chr21: 36588933-36589981 SFRS9 manual proc 1 1 5 chr14: 91136604-91139705 POLR3G proc 1 1 2 chr3: 133590336-133594125 KIAA1333 dup 1 7 chr9: 75278688-75279979 DPP3 manual proc 3 1 chr22: 40726971-40728762 SLC25A5 manual proc 1 1 2 chr5: 114875647-114877498 CCT5 proc 1 1 1 1 chr18: 22090016-22090564 FAM60A proc 3 2 chr9: 34308269-34310028 SERPINH1 manual proc 2 1 1 chr7: 27462505-27465027 EIF4H manual proc 1 1 1 chr16: 31486617-31488548 CSDA proc 3 1 chr9: 21685064-21689997 KHSRP manual proc 3 1 chr3: 49329045-49329924 SSNA1 proc 3 9 chr4: 146516051-146518502 RTN3 proc 1 3 2 chr8: 87563050-87564438 NTAN1 auto dup 1 1 6 chr7: 104957816-104958449 RNF181 proc 3 1 1 chr19: 62378395-62379706 PTCD3 dup 2 1 chr9: 89871235-89875006 PNRC2 manual 2 1 chr6: 30707737-30709987 PTMA manual 2 1 chr11: 18643045-18644377 SFRS3 auto proc 2 1 chr7: 138506992-138509638 MSL3L1 manual dup 2 1 chr3: 197148302-197149669 PPP4R2 manual dup 2 1 chr2: 204206408-204208995 ZNF207 manual proc 2 1 chr2: 179027517-179028802 NUDC manual proc 2 1 chr17: 24552608-24554860 TWF1 auto proc 2 1 1 chr17: 22433702-22435031 TUFM proc 3 1 1 1 chr12: 1843255-1844894 LAMP1 auto proc 4 1 chrX: 114805474-114806874 ASS1 manual proc 1 2 1 chr2: 162065731-162069847 AHCTF1 manual proc 1 2 1 chr1: 16006265-16007067 UQCRH manual 2 2 chr2: 43761451-43762368 ZFP106 manual frag 2 2 chr6: 158577413-158579430 SRP72 manual dup 2 2 chr3: 15895007-15896926 IMPDH1 manual dup 1 2 1 chr1: 245410530-245415024 PEX5 manual proc 1 2 1 chr13: 18423767-18425026 PHF2 manual dup 1 2 2 chr1: 104417120-104419481 THAP3 manual proc 1 2 2 chrX: 40578772-40580026 MKRN1 dup 1 2 chr19: 32986379-32989682 BC040831 proc 1 2 chr10: 121370445-121373045 RAD1 manual proc 1 2 chr1: 212722108-212723497 AP3S1 manual proc 1 2 chr1: 226368927-226369874 FAM96A manual proc 1 2 chr16: 17095569-17097803 LYRM2 dup 3 1 chr1: 144990000-144992583 IGF2BP2 manual proc 3 1 chr3: 44595235-44597668 MPRIP manual dup 1 1 9 chr12: 109351042-109353797 HMGA1 proc 1 1 1 2 chr7: 16870050-16872687 RAD17 manual proc 3 3 3 chr4: 358246-359943 ZNF43 dup 1 2 1 chr16: 46156574-46158361 EIF4B proc 1 2 1 chr9: 16765715-16765767 LSM1 manual proc 2 3 1 2 chr15: 43132056-43133113 YWHAZ proc 2 1 5 chr5: 114752657-114755023 CTNNA1 proc 1 5 chrX: 73266994-73269840 DDX3Y manual dup 1 2 4 chr19: 14461030-14461871 SNRPG proc 3 1 8 chr2: 135985004-135986146 G3BP1 manual proc 1 1 2 1 chrX: 85225950-85227916 STIP1 manual proc 4 1 3 2 chr11: 86208209-86209928 MOBKL3 proc 2 2 chr13: 28191258-28194994 CYP51A1 manual dup 2 2 chr3: 171262714-171264755 SETD8 proc 1 3 1 2 chrX: 13306389-13307499 GPX1 manual proc 1 3 1 2 chr11: 133498167-133500014 PTP4A2 proc 4 1 chr1: 245420253-245420689 ZNF720 manual proc 3 1 chrX: 65092271-65093777 RBMX manual proc 2 2 1 chr7: 63832277-63834664 MPZL1 manual proc 1 3 chr15: 91140001-91141446 ASB9 proc 2 8 chr10: 135007719-135008625 BANF1 manual frag 1 2 2 chr2: 171165069-171166985 HMGB1 manual proc 1 4 1 chrX: 73296169-73299018 MKRN1 manual proc 3 2 chr6: 31351298-31355026 USP8 manual proc 3 2 chr10: 21952707-21955029 HNRNPR manual proc 3 2 chr7: 158107538-158109026 THAP5 manual frag 1 2 2 1 chr15: 57756054-57757383 PIGH proc 3 3 chr18: 55835065-55835698 FAM60A auto proc 3 3 chr22: 37448047-37449602 PRDX3 manual proc 3 3 chr22: 22320853-22325031 ASL manual dup 2 2 7 chr10: 13238600-13239995 BTBD7 manual dup 2 3 1 chr7: 46005000-46007016 TTC4 manual proc 1 1 2 1 3 chr15: 91139708-91140030 ASB9 proc 2 2 4 chr5: 68645003-68645660 CFL1 proc 2 11 chrX: 120164368-120165004 HSPA8 manual 3 2 1 chr17: 39660007-39663513 SHC1 proc 3 2 2 2 chr17: 26359119-26359614 YWHAE dup 1 3 2 chr1: 76938038-76939270 TPI1 manual proc 2 2 2 1 chr4: 113966768-113968338 TAF4B auto frag 4 1 chr13: 76456888-76460017 DHX9 manual proc 4 1 chr13: 98665103-98666182 H2AFZ manual proc 4 1 chr10: 64650560-64652770 TATDN1 manual proc 4 1 chr9: 30678968-30680030 RBMX manual proc 2 3 1 chr13: 88810056-88813657 SP3 manual proc 1 4 chr10: 70062143-70062538 FAM36A manual 1 3 2 3 chr5: 172445309-172447866 CDC42 proc 4 2 chr9: 98527969-98529661 MKRN1 manual dup 1 1 3 4 chr12: 86700634-86702602 MKRN1 auto proc 1 4 2 chr7: 117310724-117311343 SFRS3 manual 3 3 chr7: 56261370-56264649 CCNJ manual proc 1 4 1 chr6: 131545798-131548372 DPF2 manual proc 1 1 4 chr12: 3820029-3825029 OTUD4 proc 5 1 chrX: 73719066-73719697 PABPC1 manual frag 5 1 chr1: 241495850-241498178 FCF1 manual proc 5 1 chr1: 16885318-16888034 PDE4DIP manual 5 4 1 chr12: 99496386-99499915 PIGA proc 1 2 4 chrX: 79711705-79715004 HK2 manual proc 1 1 4 1 1 chr8: 107777994-107779579 TAGLN2 proc 1 1 5 1 chr1: 177437318-177437893 EIF4A1 manual frag 6 3 chr13: 76460074-76462820 DHX9 manual proc 6 1 chr10: 94417431-94419676 EIF2S2 manual proc 6 1 chr2: 191565081-191567610 RAB1A manual dup 3 4 4 chr1: 176981907-176983662 PTPN2 manual proc 1 6 chr5: 72327995-72329739 DULLARD proc 6 2 chr11: 61895019-61899450 RCC2 proc 2 3 15 chr10: 23465825-23468573 YWHAZ manual 6 3 2 chr10: 107436038-107439382 YWHAZ manual proc 1 4 4 1 chr7: 98432519-98435031 RNF14 manual proc 6 4 chr3: 97977193-97979955 CDV3 auto proc 1 2 5 1 chrX: 41417881-41420027 YWHAZ manual 1 3 5 chr17: 20456347-20460008 DEF8 manual proc 1 6 1 1 chr14: 70866169-70867395 PDZD11 proc 7 1 chr5: 37245024-37248385 OFD1 auto proc 1 7 chr12: 3818860-3819919 OTUD4 proc 3 3 5 1 chr7: 6647990-6650019 GZF1 manual 3 6 1 chr12: 110590068-110592654 PCNP auto proc 1 8 2 chr20: 17940242-17942547 PTMA manual 2 6 5 4 chr7: 150830163-150832517 ETF1 proc 9 2 chr22: 24075369-24076698 PHF10 manual proc 1 1 8 1 3 chr6: 53207834-53209186 HMGB1 manual proc 6 8 chr7: 32762364-32763505 DPY19L2P2 manual dup 2 13 7 7 chr14: 54835005-54835966 CHMP4B proc 3 4 17 1 chr22: 29627969-29630029 EIF4H manual proc 3 3 5 12 1 chr17: 4072185-4075029 RYK proc 2 7 9 1 chr6: 160051470-160055015 HNRNPH2 manual proc 2 6 10 1 chr4: 129295826-129297562 FOSL1 proc 3 1 13 1 chr11: 6465021-6467394 VDAC1 dup 2 11 3 1 chr12: 13046376-13049181 HTR7 proc 2 4 3 6 1 chr12: 51833223-51834834 EIF4A1 auto proc 7 7 1 1 chr15: 91077671-91078734 H2AFV auto proc 15 1 chr16: 14920001-14923862 PKD1 dup 2 2 3 7 1 chr13: 40090629-40094438 RNF6 manual dup 2 2 7 2 1 chr7: 144911241-144912979 DPY19L4 manual proc 1 4 3 4 1 1 chr21: 31920001-31923002 FBXW11 manual proc 3 2 4 4 1 chr22: 34623087-34624393 NDUFA9 manual proc 1 12 1 chr2: 101256951-101257613 PPIA dup 2 1 7 2 1 chr12: 54660003-54663591 RAB13 auto 1 5 6 1 chr2: 85421131-85422577 PEBP1 proc 7 1 1 3 1 chrX: 81638952-81640007 EIF3J manual frag 7 3 2 1 chr15: 63850100-63851589 DNAJB14 auto proc 1 7 4 1 chr17: 78125786-78128688 ARL2BP dup 2 2 7 1 chr8: 48585762-48587345 NSFL1C proc 3 1 5 2 1 chr11: 66285096-66286445 C1QBP auto proc 2 9 1 chr7: 72033364-72034127 POMZP3 dup 1 4 3 2 1 chr7: 30528821-30529744 FLJ00278 manual 7 3 1 chr12: 70528835-70530029 MRS2 proc 7 3 1 chr17: 27461314-27463910 WDR45L auto proc 1 1 4 1 3 1 chr10: 79160515-79164753 ZNF532 manual dup 1 9 1 chr11: 232267-233719 SRP19 dup 7 2 1 chr8: 59500000-59502148 PTPN11 dup 8 1 1 chr19: 14042134-14043294 EEF1D auto frag 7 1 1 1 chr15: 54085179-54086686 CNOT6L auto proc 1 1 3 4 1 chr10: 127345241-127346621 ALDOA manual proc 7 1 1 1 chr19: 45140233-45141668 PRR13 auto 1 1 4 2 1 chr17: 72157677-72159762 PTMA auto 5 3 1 chr5: 177525251-177526202 APOA1BP proc 5 1 1 1 1 chrX: 41420046-41420852 YWHAZ manual 1 1 6 1 chr3: 52382585-52384174 PPP2R5C proc 1 6 1 1 chr1: 245429261-245429363 ZNF720 manual 2 4 2 1 chr5: 107088630-107089995 USP7 proc 5 3 1 chr4: 118715123-118716642 NT5C3 manual proc 2 4 2 1 chr22: 21935039-21937130 FBXW4 manual proc 3 5 1 chr5: 175667341-175669888 BRCC3 dup 6 1 1 chr14: 95758990-95760012 CKS1B proc 3 2 2 1 chrY: 11781394-11785025 LOC389834 proc 3 1 3 1 chr12: 6457164-6459964 PKP2 proc 7 1 chr21: 46897231-46898445 DSTN manual frag 1 4 2 1 chrX: 48519005-48520014 ACAA2 manual proc 3 4 1 chr2: 197835918-197836621 ATP5G2 manual proc 7 1 chr15: 97615266-97617895 HSP90B1 proc 1 2 1 1 1 1 chr8: 82692562-82693415 NIPA2 proc 1 2 3 1 chr4: 145986182-145988340 HSPD1 auto proc 3 2 1 1 chrX: 70451371-70452584 ZCRB1 manual dup 2 1 3 1 chr8: 30225003-30227051 TAGLN2 auto proc 2 4 1 chr2: 32280035-32282728 DDX50 manual dup 4 2 1 chr2: 84856616-84858887 LDHA manual proc 1 1 4 1 chr1: 245420126-245420978 ZNF682 manual proc 5 1 1 chr6: 36167532-36168612 NUDT5 manual proc 6 1 chr17: 2436284-2437919 EIF4A1 dup 1 1 2 1 1 chr12: 78225570-78226943 REST dup 1 1 3 1 chr2: 20355007-20355544 RP9 dup 1 4 1 chr16: 18386391-18389697 PKD1 dup 2 3 1 chr3: 133588073-133590018 KIAA1333 dup 5 1 chr11: 82597892-82598941 CKS1B proc 1 3 1 1 chr11: 122335815-122337882 ATP5F1 proc 1 4 1 chr15: 33171848-33172885 U2AF1 proc 1 4 1 chr19: 3821749-3823145 FTL auto proc 3 2 1 chr1: 96685035-96686396 EEF1A1 manual proc 2 2 1 1 chr10: 59642034-59642720 TPT1 manual proc 1 3 1 1 chr7: 55672416-55674246 CDC42 manual proc 4 1 1 chr7: 5566916-5567375 S100A11 manual proc 4 1 1 chr6: 147770007-147774161 YAP1 manual proc 2 3 1 chr3: 155553099-155554758 DDX50 proc 1 2 1 1 chr14: 57677677-57678048 UBA52 proc 3 1 1 chr2: 91130114-91132611 TMEM128 manual frag 3 1 1 chrX: 67920024-67922986 SERBP1 manual dup 1 3 1 chr22: 22600024-22604137 KLHL5 manual dup 1 3 1 chr3: 36783146-36785030 HSPD1 manual proc 1 2 1 1 chrX: 49283282-49284875 VDAC1 manual proc 3 1 1 chrX: 65635098-65636615 PKM2 manual proc 1 3 1 chr9: 130067782-130069317 FLJ00278 dup 3 1 chr15: 34692846-34694996 TPM3 proc 1 2 1 chr4: 79320311-79322415 SERBP1 proc 1 2 1 chr9: 37625488-37627344 RAB1B manual 3 1 chr16: 4552399-4553233 SUB1 proc 3 1 chr3: 171145011-171147501 FHL1 proc 3 1 chr4: 166544280-166544941 HADHA proc 3 1 chr9: 138826841-138829981 NCL manual dup 1 1 1 1 chr16: 21692-25029 IL9R manual dup 3 1 chr2: 202772424-202775011 DAZAP2 manual proc 1 1 1 1 chr7: 88106317-88107757 EEF1A1 manual proc 1 1 1 1 chr2: 222535085-222537390 HSPA9 manual proc 2 1 1 chr7: 143975043-143976509 EEF1A1 manual proc 2 1 1 chr1: 64080787-64082020 CFL1 manual proc 1 2 1 chr21: 36345013-36346248 FAM80B manual proc 1 2 1 chr20: 32452814-32454340 CDC42 manual proc 1 2 1 chr3: 25771373-25774090 TAF9B manual proc 3 1 chr1: 78085216-78088009 CCDC55 manual proc 2 5 20 2 chr6: 143705076-143706473 PARL manual proc 3 12 3 1 7 1 1 chr3: 122007401-122009653 NAP1L1 auto proc 1 5 9 6 2 chr9: 126952546-126954985 PRPS1 manual proc 6 4 11 2 chr9: 34911199-34912896 YWHAZ manual proc 1 9 7 3 1 1 chr19: 58005048-58009278 PABPN1 proc 1 3 5 10 1 1 chr3: 95276627-95278752 RBBP4 proc 1 2 11 4 2 chr12: 41110881-41113477 FXR1 proc 1 2 11 4 2 chr15: 51016593-51017949 EEF1A1 proc 8 6 3 2 chr4: 88053138-88055031 ARPC1A dup 5 10 1 1 chr6: 30262288-30264297 PAIP1 manual dup 1 9 5 2 chr3: 52202197-52204001 ALDOA dup 9 1 2 2 1 1 chr9: 12962422-12963578 PRDX1 manual proc 3 4 2 1 4 2 chr12: 19985423-19989724 TCP1 proc 6 1 4 2 chr3: 115086410-115088196 DULLARD auto proc 4 5 1 1 2 chr7: 7986381-7988620 PPIL4 manual dup 10 1 2 chr17: 42855745-42858503 NFE2L3 dup 2 8 2 chr15: 73400772-73402108 ANP32B proc 5 4 1 2 chr1: 218493241-218494999 MORF4L1 manual proc 5 4 1 2 chr2: 25898653-25900030 PTGES3 manual proc 6 4 2 chr3: 53070978-53074165 SERBP1 proc 2 5 2 2 chr8: 62011957-62014951 NASP proc 1 4 4 2 chr17: 60204622-60205031 LOC201175 proc 2 7 2 chr22: 40833082-40834984 OLA1 manual proc 1 1 1 6 2 chr2: 74498320-74499480 HMGA1 manual 1 2 4 1 2 chr22: 22040076-22042678 CES7 manual 7 2 chrX: 130608331-130609932 HDGF manual frag 3 1 1 2 2 chr1: 158906538-158909903 SET manual proc 2 5 2 chr9: 22001477-22002779 UBA52 manual proc 4 3 2 chr11: 91708751-91709133 NDUFB11 manual proc 3 4 2 chr22: 22045609-22049946 CES7 manual 6 2 chr13: 64430032-64431456 LGMN manual dup 2 3 1 2 chr14: 63130269-63131835 GCAT auto proc 4 2 2 chrX: 120165030-120166529 HSPA8 manual proc 2 1 2 1 2 chr1: 207507608-207508364 ATP5G2 manual proc 1 3 1 1 2 chr11: 92908039-92909143 SRP14 proc 2 1 2 2 chr3: 23895319-23895949 ARL4A manual proc 1 4 2 chr9: 5100700-5103470 TCF3 manual proc 5 2 chr1: 218507681-218508028 AURKA manual proc 5 2 chr5: 43530817-43532401 EEF1A1 proc 1 2 1 2 chr22: 22031558-22032127 CES7 manual 4 2 chr18: 54508763-54509828 MRPL37 proc 4 2 chr5: 14850010-14851722 RBBP4 proc 4 1 1 chr2: 127030021-127032314 YWHAZ manual proc 1 3 2 chr6: 25131126-25132842 ASS1 manual proc 1 3 2 chr6: 111285905-111288987 CNN2 manual proc 3 1 2 chr10: 66255316-66256651 ANXA2 manual proc 4 2 chr1: 51395688-51396740 CFL1 manual proc 2 1 1 1 1 chr17: 71733295-71734754 ATF4 manual 2 1 1 1 chr7: 20588278-20589374 EEF1A1 manual proc 1 1 1 2 chr2: 236455494-236455892 TMSB10 manual proc 1 2 2 chr3: 187961542-187964137 PSMD10 manual proc 3 2 chr4: 10982554-10984464 RNPS1 proc 5 10 5 1 11 2 1 chr17: 11959531-11959908 DYNLT1 proc 12 3 5 7 3 chr1: 106235172-106236952 MATR3 manual proc 3 4 8 7 4 1 2 chr11: 18465871-18469227 YWHAB proc 1 4 9 7 3 chr22: 23903543-23904988 STMN3 manual proc 10 4 7 1 2 chr1: 166055742-166056259 FAM177A1 manual dup 3 8 1 7 3 chr16: 68346815-68349469 NONO proc 1 6 6 4 1 2 chr9: 88816231-88818084 CDC20 manual proc 1 1 3 1 11 3 chr1: 233967900-233969581 LDHA manual proc 1 2 10 3 3 chr7: 65525025-65526430 SKP1 manual proc 3 1 6 6 3 chr8: 55046759-55049918 ESF1 proc 1 8 4 3 chr13: 44861259-44863071 RCN1 manual 1 3 1 1 7 1 2 chr12: 119766955-119768000 ARF1 auto proc 6 2 1 4 1 1 1 chr20: 60947228-60948154 DPH3 manual proc 4 4 3 2 2 1 chrX: 53210000-53210656 SUV39H2 manual frag 1 8 3 2 1 chr17: 20628146-20629946 SCD manual proc 9 1 2 1 2 chr5: 68644250-68645023 CFL1 proc 1 2 6 3 chr17: 27578894-27579439 UBL5 proc 3 3 3 3 chr1: 72512203-72513454 GDI2 manual frag 1 3 2 3 3 chr1: 240223113-240224419 CFL1 manual proc 3 2 3 1 3 chr3: 139081781-139083983 HSPA8 proc 2 1 3 1 1 3 chr12: 55190981-55193352 HSPD1 proc 3 4 1 3 chr21: 38796179-38796358 SNRPG manual proc 6 1 1 1 2 chrX: 65210128-65212872 EIF4B manual proc 1 1 2 2 3 chrX: 51683397-51683809 UCRC manual proc 1 1 4 3 chr8: 30215043-30218410 HSPA8 dup 2 2 1 3 chr17: 30756783-30758835 DTWD2 proc 1 1 2 1 3 chr12: 48067082-48070015 FGFR1OP2 proc 1 3 3 chr1: 218865561-218868015 HDAC1 manual dup 4 3 chr4: 136186068-136187470 EEF1A1 dup 1 3 chr11: 29253864-29254659 EEF1A1 proc 1 3 chr4: 4946239-4947833 LDHA auto proc 1 3 chr2: 231530573-231530995 FAM36A manual proc 1 3 chr12: 17035000-17036276 EEF1A1 proc 3 chr2: 231145010-231146919 TPM3 manual proc 3 chr1: 38947029-38949502 HSPA5 manual proc 3 chr2: 48712985-48713883 TPT1 manual proc 1 2 chrX: 115766164-115766603 PRPF4B manual frag 5 8 7 3 16 2 2 chr1: 89341252-89343268 PTGES3 manual 10 10 12 1 1 2 chrX: 135755159-135758921 RAB28 manual proc 4 2 8 14 1 3 chr19: 35220001-35221268 TAF9 auto proc 5 5 3 13 4 chr12: 74737397-74739842 DENR proc 1 11 11 4 chr3: 48272166-48273216 MRPS18A manual proc 1 8 14 4 chr12: 9283162-9284461 PTMA dup 1 10 7 1 4 chr3: 27649231-27650012 TPM4 manual frag 3 7 3 6 3 1 chr7: 124460752-124462651 EEF1G manual dup 4 2 7 1 5 3 1 chr3: 157187740-157189549 SET proc 14 3 1 4 chr1: 203861013-203862993 GABARAP manual dup 1 1 16 4 chr22: 19134094-19135031 KLHL12 manual proc 1 2 14 4 chr7: 39575135-39576400 TXNDC1 manual proc 4 2 4 6 4 chr4: 74183155-74184968 HMGA1 dup 1 1 6 7 3 1 chr17: 30848980-30850029 TAF5L proc 2 4 6 3 4 chr19: 15881767-15883707 IPMK proc 1 2 4 8 4 chr7: 151694812-151694991 PSPH proc 2 11 1 1 2 2 chr17: 10560021-10560742 MAGOH proc 14 4 chr20: 48963622-48964977 PSMD10 manual proc 2 8 4 3 1 chr19: 18002173-18005024 CS proc 1 5 4 2 4 chrX: 113915399-113917620 HSPA8 manual proc 9 2 4 chr17: 30850001-30851322 TAF5L proc 2 2 4 2 4 chr6: 86193656-86194482 TPT1 manual proc 4 4 2 4 chr14: 64815693-64817730 PTBP1 auto dup 2 1 5 1 4 chr4: 98042943-98043372 COX7A2 auto proc 1 1 2 1 4 1 3 chr2: 138761156-138762932 YWHAE manual proc 4 2 1 2 4 chrX: 100676203-100679915 PRKCI manual proc 2 7 4 chr4: 39650588-39652334 PABPC1 dup 2 3 1 2 4 chr12: 19500335-19502091 EEF1A1 proc 1 4 3 4 chr12: 4076871-4079190 HSPA8 dup 2 3 1 1 4 chr1: 201002645-201003292 COX7C manual proc 2 1 3 4 chr9: 119885003-119885562 TPT1 manual proc 2 2 2 3 1 chr4: 22337134-22338823 CDC42 auto 1 2 2 4 chr13: 48243346-48243963 PSME2 manual proc 3 1 1 4 chr10: 32840157-32840929 C1D manual proc 1 1 3 4 chr3: 39375064-39376459 EEF1A1 manual proc 1 3 4 chr6: 109335327-109335840 ATP5J2 manual proc 1 2 1 1 2 chr13: 27686701-27688179 EEF1A1 manual proc 1 1 4 chr3: 120732546-120733113 CSRP2 proc 4 chrX: 74880003-74883639 TTC3 manual proc 11 8 4 5 26 1 4 chr16: 11905084-11905547 COX6C proc 14 1 7 4 4 4 1 chr1: 52606731-52607671 PLA2G12A manual proc 5 4 6 15 5 chr6: 158950293-158952897 TATDN2 manual proc 4 6 10 1 6 4 1 chr5: 96416174-96418578 SET auto proc 3 10 9 3 5 chr1: 89067086-89067800 TCEB1 manual proc 3 3 11 7 5 chr12: 12155020-12156368 PTMA auto frag 1 10 10 2 2 3 chr7: 104095351-104099270 EIF4B manual proc 1 9 8 5 5 chrX: 114843363-114844764 EEF1G manual proc 3 5 6 1 6 5 chr2: 61016549-61018625 NONO manual dup 2 5 9 4 5 chr17: 37935489-37939966 PTP4A2 proc 3 9 4 3 5 chr12: 67322298-67323260 ATP5H proc 1 1 11 5 5 chr9: 32935789-32937584 ASS1 manual proc 1 2 9 4 5 chr17: 60205003-60209312 LOC201175 proc 6 8 5 chrX: 25573624-25574445 RANBP1 manual 3 4 4 5 chr17: 64826385-64826952 SNRPG proc 1 8 1 5 chr14: 35420023-35420673 EWSR1 proc 1 3 4 1 5 chr22: 22070000-22074479 ZDHHC8 manual frag 9 5 chr9: 6656022-6660031 RNF2 manual proc 1 4 3 5 chr1: 245460000-245461944 HSPA8 manual proc 1 2 2 1 1 5 chr9: 6660006-6664836 RNF2 manual proc 1 3 3 5 chr9: 14910713-14912555 LDHA manual proc 1 1 4 1 1 4 chr3: 185226809-185228146 EEF1A1 manual dup 2 1 1 5 chr1: 42738096-42738591 TMSB4X manual 1 1 5 chrX: 23003631-23004877 FAM3C manual 10 12 6 17 9 1 1 4 chr22: 24375001-24378128 YES1 manual dup 8 10 8 8 10 1 2 1 2 chr3: 48306896-48308964 FCF1 manual proc 3 10 6 13 1 4 1 chr2: 132196980-132198589 TOMM40 manual proc 7 8 6 2 6 1 5 chr1: 116875720-116878445 NAP1L4 manual proc 5 1 10 3 1 5 1 chr6: 5917621-5919864 PKM2 manual proc 8 3 8 1 4 1 1 chr15: 19186009-19190031 PAK2 auto proc 4 15 6 chrX: 30558147-30559009 FTL manual proc 1 8 3 4 2 1 5 chr3: 182442769-182443381 FAU proc 2 1 3 6 5 2 4 chr6: 144563059-144563906 TPT1 manual proc 1 6 5 1 4 5 1 chrX: 44377591-44379921 CTF8 manual proc 3 5 3 2 1 5 chr1: 169906030-169906835 PFN1 manual proc 1 1 6 chr12: 32770077-32771796 NAP1L1 proc 4 7 11 18 5 2 chr10: 75161319-75163908 DUSP8 manual proc 7 1 5 24 1 6 chr15: 19190000-19191609 PAK2 auto proc 3 2 31 1 1 5 chr17: 25420266-25421375 STX18 proc 8 4 2 7 14 1 1 3 2 chr9: 97948095-97950029 EIF4B manual proc 3 13 10 9 2 5 chr17: 60380103-60384663 SLC16A6 dup 5 3 10 1 15 1 3 3 chrX: 70555627-70557712 PABPN1 manual proc 3 11 1 18 5 2 chr18: 1350751-1353998 ATAD1 auto dup 3 11 4 7 7 1 1 2 1 2 chr7: 137738291-137739988 PTMA manual frag 3 16 9 4 2 5 chrX: 73340516-73344880 RAB11FIP1 manual proc 4 9 18 4 3 chr3: 40612582-40613978 EEF1G manual proc 3 13 3 6 1 5 1 chr4: 166545018-166547102 HADHA proc 1 14 7 chr7: 10457157-10459773 HSPA8 manual proc 4 4 5 1 6 1 chr5: 43622114-43624741 AMD1 auto proc 1 1 5 4 5 2 chr10: 76705756-76706390 HMGA1 manual 1 8 2 5 chr6: 74058239-74059970 EIF3E manual proc 2 9 9 1 16 4 1 3 chr15: 88619130-88620026 PERP proc 14 1 7 14 1 1 6 chr22: 24373154-24375027 YES1 manual dup 3 9 24 4 4 chr12: 6864001-6865025 DSTN manual proc 2 17 6 2 9 2 5 1 chr12: 62501627-62504537 PABPC1 proc 9 6 3 2 13 4 4 chr1: 75980428-75983188 DLST manual dup 6 11 1 12 6 2 chr14: 61368169-61368862 COX4I1 proc 4 1 7 6 4 3 1 chr10: 42335001-42336262 ZNF37A manual dup 6 15 11 1 24 1 5 3 chr1: 145141125-145143358 CCT8 manual proc 7 13 9 1 22 3 4 2 chr5: 177330758-177333479 SUDS3 auto proc 2 3 18 9 chr11: 119196989-119198204 BAT1 proc 6 6 1 5 5 4 chr10: 120681594-120682842 LDHA manual frag 2 4 4 3 1 1 5 1 1 chr9: 124488119-124489981 TLK1 manual dup 1 3 4 1 2 8 1 chr2: 234438687-234440030 MSL3L1 manual proc 19 16 4 14 45 2 5 1 2 chr3: 180460196-180461897 LRRFIP1 proc 12 8 10 4 31 5 5 chr11: 33051914-33054815 PIGC auto proc 7 18 11 2 19 1 5 4 chr20: 3952190-3953301 FTL manual 4 16 4 1 7 1 3 5 1 chr2: 234440001-234441782 MSL3L1 manual proc 16 18 4 12 30 1 1 5 1 3 chr2: 162640152-162642586 TIMM8A manual proc 1 34 11 chr1: 114880845-114882611 PKM2 manual proc 9 5 5 3 1 3 5 1 2 chr11: 43875453-43878110 SEC14L1 auto proc 11 7 11 8 26 1 5 6 chr22: 19135000-19137681 KLHL12 manual proc 10 2 9 1 31 1 5 6 chr22: 30995341-30999218 CPSF1 manual proc 4 1 1 2 38 12 chr10: 71593210-71594625 CALM2 manual proc 9 8 5 6 13 1 1 11 chr3: 117845959-117848342 BZW1 auto frag 18 20 10 14 20 2 3 5 3 3 chr18: 12056629-12058570 SSBP4 dup 18 15 5 12 18 3 1 6 7 chrX: 122077782-122079346 MRRF proc 20 17 4 5 19 7 1 7 4 chr17: 60176781-60178361 ASCC3L1 dup 28 15 10 14 54 2 3 3 13 chrX: 74875425-74880031 TTC3 manual proc 28 15 8 10 55 4 4 16 chr17: 63636429-63636974 DQ587552 dup 39 9 6 19 50 10 2 4 2 10 chrY: 11770408-11775026 FLJ00219 dup 29 2 4 20 62 8 6 3 11 chr11: 113145499-113147696 COX7A2L proc 31 13 6 14 33 6 2 6 1 14 chr5: 75708184-75708770 SNRPC auto proc 48 17 11 21 51 7 2 8 3 11

All publications, patents, patent applications and accession numbers mentioned in the above specification are herein incorporated by reference in their entirety. Although the invention has been described in connection with specific embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications and variations of the described compositions and methods of the invention will be apparent to those of ordinary skill in the art and are intended to be within the scope of the following claims. 

We claim:
 1. A method of screening for the presence of breast cancer in a subject, comprising (a) contacting a biological sample from a subject with a reagent for detecting the level of expression of ATPase, aminophospholipid transporter, class I, type 8A, member 2 pseudogene (ATP8A2-Ψ); and (b) detecting the level of expression of said ATP8A2-Ψ in said sample using an in vitro assay, wherein an increased level of expression of said ATP8A2-Ψ in said sample relative to the level in normal breast cells is indicative of breast cancer in said subject.
 2. The method of claim 1, wherein the sample is selected from the group consisting of tissue, blood, plasma, serum and breast cells.
 3. The method of claim 1, wherein detection is carried out utilizing a method selected from the group consisting of a sequencing technique, a nucleic acid hybridization technique, a nucleic acid amplification technique, and an immunoassay.
 4. The method of claim 3, wherein the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification.
 5. The method of claim 1, wherein said breast cancer is luminal breast cancer.
 6. The method of claim 1, wherein said reagent is selected from the group consisting of a pair of amplification oligonucleotides and an oligonucleotide probe.
 7. A method of screening for the presence of prostate cancer in a subject, comprising (a) contacting a biological sample from a subject with a reagent for detecting the level of expression of coxsackie virus and adenovirus receptor pseudogene (CXADR-Ψ); and (b) detecting the level of expression of said CXADR-Ψ in said sample using an in vitro assay, wherein an increased level of expression of said CXADR-Ψ in said sample relative to the level in normal prostate cells is indicative of prostate cancer in said subject.
 8. The method of claim 7, wherein the sample is selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions and prostate cells.
 9. The method of claim 7, wherein detection is carried out utilizing a method selected from the group consisting of a sequencing technique, a nucleic acid hybridization technique, a nucleic acid amplification technique, and an immunoassay.
 10. The method of claim 9, wherein the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification.
 11. The method of claim 7, wherein said cancer is selected from the group consisting of localized prostate cancer and metastatic prostate cancer.
 12. The method of claim 7, wherein said reagent is selected from the group consisting of a pair of amplification oligonucleotides and an oligonucleotide probe.
 13. The method of claim 7, wherein said biological sample lacks and ETS gene fusion.
 14. A method of screening for the presence of prostate cancer in a subject, comprising (a) contacting a biological sample from a subject with a reagent for detecting the presence of a kallikrein-related peptidase 4-kallikrein pseudogene 1 (KLK4-KLKP1) gene fusion; and (b) detecting the presence or absence of said KLK4-KLKP1 gene fusion in said sample using an in vitro assay, wherein the presence of said KLK4-KLKP1 gene fusion in said sample is indicative of prostate cancer in said subject.
 15. The method of claim 14, wherein the sample is selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions and prostate cells.
 16. The method of claim 14, wherein detection is carried out utilizing a method selected from the group consisting of a sequencing technique, a nucleic acid hybridization technique, a nucleic acid amplification technique, and an immunoassay.
 17. The method of claim 16, wherein the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification.
 18. The method of claim 14, wherein said cancer is selected from the group consisting of localized prostate cancer and metastatic prostate cancer.
 19. The method of claim 14, wherein said reagent is selected from the group consisting of a pair of amplification oligonucleotides and an oligonucleotide probe.
 20. The method of claim 14, wherein said KLK4-KLKP1 gene fusion is an mRNA. 